We try to avoid using things like Adobe AfterEffects for video production for several reasons.
1. Cost. It's pretty pricey, even with academic/student discounts. Granted, some fansub groups just get it from non-traditional sources anyway, but since I don't intend to make an argument about morality, I'll just let the facts stand that it is pricey and it's available through non-traditional channels.
2. AviSynth. AviSynth can do a lot of what AfterEffects can do. For example, one of the more common uses for AfterEffects in fansubbing is to mask Japanese names on hospital signs and replace them with English ones. That can be done in AviSynth and rotation commands in TextSub.
There are, of course, certain things that AviSynth and TextSub are not capable of doing that AfterEffects can do. However, most of them get into the "gaudy and excessive", which was pioneered by AnimeJunkies a while back. I started fansubbing when they were at their peak; I'll tell you what happened in a later post.
3. The challenge to do something using free tools versus an expensive tool is always a rewarding experience. I'm still trying to figure out how to do handwritten text using TextSub and AviSynth. :)