Everything goes in cycles. Rule changes have a big effect. Guys like Bill Walsh who exploit them first get a jump on the rest, but eventually everyone catches up and figures out how to stop something because everyone is running it. Interesting article on the spread:
Something of note is that the guys who have really excelled at it have been running a form of the spread as early as 6th grade, so really it's easy to see why the transition in the pros is difficult, these guys have grown up playing this way. I think the next few years will determine how many teams run it in college, at least big time programs. If there isn't a guy who comes from the spread that has success in the NFL soon, I think you'll see teams that run a pro-style offense have a distinct recruiting advantage, at least at the QB position because guys will want to be prepared to succeed in the NFL.
I think this will happen though because until recently the teams running it were doing so to make up for a lack of talent. More big time schools with big time talent are running it now and at some point QBs that are just destined to be great will come out of that offense and the whole spread argument will be a thing of the past. I have a hard time beleiving that Bradford, McCoy, and Tebow will ALL be busts so it could be very soon.