Obviously, the attacks were very carefully planned and timing was essential. While later flights may have ensured greater loss of life, early flights accomplish at least two things:
1) Fewer pax on board, so less potential interference (they apparently took pains on some flights to mace the FC pax, etc.)
2) Security is more lax in the am -- fewer staff, less scrutiny, etc.

I agree that the on-time departure was also important, if only to ensure that the flights could reach their targets before any response could be mounted. Again, timing was carefully considered.