Because amphetamines can be very useful for short term bursts, but are generally not a good idea in real warfare, which usually tends to involve more long term operations. They are useful in small amounts to keep soldiers awake for long hours, of course, but if you give soldiers enough meth to blast through an enemy line, it'll do the job, but then the soldiers drop from exhaustion and can't hold their positions, which is actually even worse. War is a lot different than a movie where Rambo mows down enemies with his machine gun.
Now, for pilots, go/no-go pills make sense, you want these guys as alert and awake as possible on a moment's notice, to last for a few hours, after which they return to their airbase/carrier. Fuel and ammunition create enough of a limitation on the time spent in combat so as to make medication useful.