For the record, I'm a witch. And the Burning Times were a part of our history which we constantly remind ourselves of, lest we grow complacent in this time of growing tolerance.
That having been said...
Christianity's stance toward the established pagan religions, in the very early days, was not one of persecution, but rather one of embrace and extend. Yes, it was very similar to Microsoft's business strategy. Christians were a minority in the years immediately following the death of Jesus, and for survival's sake, the early missionaries chose to incorporate elements of pagan practices into their own, so that the Christian celebrations and rites wouldn't look terribly different from the pagan ones. Hence we have fertility icons (rabbits and eggs) associated with Easter, holly and evergreen trees at Christmas, All Saints' Day immediately following Samhain, and the like. It's much easier to get people to change their outlook on life when the new way isn't (at least superficially) all that different from the old one. In some parts of Europe, in fact, the pagans would attend Mass during the day along with the Christian members of the community, and then go off at night to perform their own rites, referred to as the Night Mass, or the Black Mass.
Friendly assimilation stopped working when the Christian Church realised that the most powerful covens who owned a lot of land would not be converted and would not sell their lands for any reason. The Church needed land to help consolidate its power, and the patriarchal organisation of the Christians had trouble coping with the matriarchal society of the pagans. The initial executions of witches for accusations of heresy were a power play, to have covenstead lands revert to control of the local nobility, who would in turn hand it over to the Church as a tithe. This had the additional effect of removing women from positions of landed power.
This snowballed, of course. In quite a short time, it became fashionable to accuse someone of witchcraft in order to make a play for their property. The friendly ties between the Christians and the pagans were soon forgotten, and the Black Mass became a synonym for devil worship. Many real witches died during this time, it is true. But a nontrivial number of Christians were executed during this time, as well. This is what most modern-day witches have the biggest problem with: not only were our own kind destroyed for not worshiping the Christian God, but many innocents were also slaughtered and paganism was made the scapegoat -- and that the lies and propaganda which originated in that time are still spread to this day.
Modern paganism has its radical zealots, just as any other religion or group, and like any zealots, they're the most visible and often the most annoying. But the advice which needs to go out to all, regarding all people: do not judge the whole group based on the conduct of the radical fringe.
Tiefling: No offence taken. Between your writeup and mine, the point is pretty much well laid out if the reader can filter out the emotion behind them. This is history, and there are those who wrote it, and also those who look back on it with hatred and sorrow. The "true" story will likely not ever be known -- all that we will ever have will be the official accounts and the attempts of people (like myself) to air out other "facts". And yes, some of those facts can be construed as revisionist. The truth lies somewhere between, and it's up to an individual to find it. (Unlikely as that is, in this day and age of "do the work for me and give me the results, I need instant gratification".) Arguing the point merely keeps the emotional flames high and does nothing to make progress.