Even if I agree with the fact the Cyberdemon is a tough enemy in
Doom, I remarked that when setting up a
level in which he would face the
SpiderDemon (so that they'd
shoot at each other until one of them would die), the SpiderDemon usually won so I'd rather say that the Cyberdemon is the second-toughest enemy in Doom (after the SpiderDemon).
The fact one could easily get rid of him because of the availability of a
BFG9000 in the third episode (
Inferno) would just make him look like less dangerous.