Roman religious tolerance is sometimes exaggerated. Religious groups were generally left alone as long as they seemed not to present any political or social threat; but non-traditional faiths (particularly the more outlandish Eastern imports) tended to be relegated to the outskirts of towns and were subject to the mockery of satirists and novelists. New or threatening ones were occasionally suppressed. Christianity wasn't alone.

In classical Rome, religious and public life were the same. Political power was enmeshed with religious ritual. Priests and magistrates were often the same men; Julius Caesar, who wasn't particularly devout, went to quite a bit of trouble to be elected chief priest (pontifex maximus), and the emperors always adopted the same title. Magistrates had religious duties as well as secular ones. Religious organizations were regulated surprisingly strictly; in particular, they were forbidden to keep a lot of cash on hand or to gather in large numbers, for fear that they planned some sort of insurrection. (In some ways, there's a parallel in modern Chinese governments: Realistically, the communist party leaders are probably not very interested in personal beliefs, but, with things like the Taiping rebellion in mind, they are very concerned about the political threat of new religious organizations.)

Though there was a sort of Roman orthodoxy, particularly after Augustus, Roman religion was very broad and very plastic. It generally accommodated foreign gods (though it was likely to eventually absorb them as aspects of existing deities) and rituals. Roman rulers were therefore pragmatic about things like respecting the faiths of conquered peoples: They weren't on a crusade and weren't eager to unnecessarily antagonize restive frontier peoples. At the same time, though, they were prepared to come down fairly hard on religions that seemed genuinely incompatible with the state religion. This included sects that:

  • were just distasteful (like the Gaulish druids, suppressed by Claudius on grounds that they practised human sacrifice);
  • were likely to be the centre of nationalist sentiment (arguably a more important reason for the eradication of those druids);
  • were linked to some kind of social disorder (like the cult of Bacchus outlawed in 186 BCE);
  • created closed communities, particularly ones that did not respect the Roman social order (Christianity was all the more alien and threatening because the early church preached egalitarianism at a time when the system of Roman social orders was becoming increasingly rigid);
  • insisted on strict exclusivity.

Exclusivity was a serious problem. At bottom, there were religious justifications for the way things worked in the Roman state; and even if these weren't widely believed or even much thought of, openly denying the existence of the traditional gods meant implicitly questioning Roman power and the whole order of Roman society. People whose faith prevented them from acknowledging religious festivals or otherwise going through the motions found themselves in a difficult position, and one that became much worse in the imperial period when it became good form to venerate the emperor. The Romans didn't (outside of Egypt, at least) worship the emperor per se, but they did worship dead ones that had been deified and sometimes -- more confusingly -- the "spirit" (genius or numen) of the current one. If you were a devotee of Isis or Mithras or a priest of some obscure Egyptian hippopotamus god, there was no problem; if you were Jewish or Christian, your faith forbade you to do any such thing.

Then there was simple fear and scapegoating. Nero, the first real persecutor, seems to have attacked the Christians to deflect public outrage over the fire of 64 (which he was later accused of having set himself) and his own misbehaviour. At other levels of society, it's not hard to see that the Christians might come to be hated and feared: Non-participation can be very threatening. Lurid stories came to be told of the strange, self-segregating Christians -- they killed babies1, and so on. While there's not a lot of evidence for anti-Christian pogroms, persecutions might easily have been politically popular.

The association of Christianity with Judaism didn't help either. Claudius (and he was not the first) expelled the Jews from Rome because of their "constant rioting"; according to Suetonius, "Chrestus" was to blame2. Later emperors faced a series of huge Jewish revolts in Palestine and riots in Alexandria. They came to see the independence-minded Jews as troublemakers, but left their formal persecution largely to later Christian emperors -- partly because a Jewish revolt was a much more serious threat than a Christian riot, partly because the Romans respected the antiquity of Judaism (as a modern Westerner might be more respectful of a Jain or Buddhist than a member of the wacky charismatic cult their neighbour had just started). Some writers and rulers feared the fanaticism and unruliness of both sects -- or, perhaps, the potential for trouble with cranky traditionalists within the same population.

Non-reasons for the persecutions include monotheism and other strictly theological differences. The Christians were not the empire's first or only monotheists.

* * *

The scale of the persecutions is contentious. Much of the information comes from Christian writers of the fourth century and later, and the Catholic church has always had an interest in emphasizing the demented cruelty of the persecutors and the heroism of the innocent martyrs -- most people have a vague idea that Christians were fed to lions, and anyone who's been treated to a Catholic upbringing (or spent much time in Italian churches) probably has vivid ideas of the sorts of hideous deaths involved. We can say that the persecutions did happen, in the sense that people were executed for being Christians; that there were probably eight to ten periods when they occurred; and that the scale seemed to increase as time went on.

The persecutions were of different types. The first was a sloppy attack on one of Rome's more defenceless minorities. Later ones became much more formal; under Trajan, being a Christian was illegal and there was a hearing (or, for citizens, a trial)3. By the third century the whole thing had become rather elaborate, with a standard protocol for the examinations. Generally, defendants were asked whether they were a Christian, and, if they responded in the affirmative, were given a choice between renouncing Christianity (sometimes by sacrificing to some other deity) and being executed. It has been suggested that the persecutions strengthened the church in various ways -- by giving it martyrs and a heroic past, by underlining the division between the Christian mini-society and the world at large, by impressing potential converts with the fervour of the martyrs, and by gaining sympathy among other citizens who saw Christians murdered simply for their religious beliefs.

All that said, here's a rough chronology of the persecutions:

The persecutions ended with the reign of Constantine (306-337, alone from 324), who was always sympathetic and was himself baptised on his deathbed (though he seems to have gradually converted years earlier). The short reign of Julian "the Apostate" marked the last test of Christianity, but by that time it was far too well-established to be really attacked. In the centuries that followed, the Roman and Byzantine churches established their spheres of influence, fought hard with heterodox sects over theological issues that now seem trifling or abstruse, and began, like abused children turning on the next generation, to dabble in persecutions of their own -- of the Jews, of pagans, and, increasingly, of "heretics" who rejected some part of orthodox theology.

1 This has always been a popular rumour to spread about religious sects. It was also told (by Christians) about Jews for something over a thousand years (it comes up in the Brothers Karamazov, for example), about masons, about some modern sects that have usually turned out to be pretty innocent, and about supposed "Satanic cults" that were thought to practise ritual child sexual abuse but generally turned out to not exist.

2 Suetonius may have this wrong -- it's probably too early for that sort of thing -- but it's significant that at the time he wrote (c.110) there was an idea about that Christianity was somehow linked to social disorder.

3 Trajan advises Pliny on how to go about the persecution: "These people must not be hunted out; if they are brought before you and the charge against them is proved, they must be punished, but in the case of anyone who denies that he is a Christian, and makes it clear that he is not by offering prayers to our gods, he is to be pardoned as a result of his repentance however suspect his past conduct may be." (Pliny, X.97; trans. Betty Radice)

Facts run by:
The Letters of the Younger Pliny, trans. Betty Radice, 1963.
A History of Rome, M.Cary and H.H. Scullard.
Oxford Classical Dictionary, Third Edition, 1996.
Religions of Rome, Beard, North and Price, 1998.
...among other sources.