The hop up IS just a piece of rubber which rubs the BB, yes. But this piece of rubber happens to be shoved into the barrel, blocking part of it. As you apply more hop, there is more of a blockage. Is that going to slow down or increase the speed of the projectile?
Hop WILL change the fps, sometimes by quite a significant margin, upto 10-20 fps depending on exact setup of the rifle and BB weight used. (tested regularly by myself and colleagues. Just in case physics changed overnight

)
fps will decrease when using a heavier ammo, but energy transferred to the target will be greater with heavier BBs, even if it had a faster fps readout with a lighter BB.
ALWAYS chrono on .2's or at the very least let the guy chronoing know what weight you have loaded (313fps on.25's is the same energy level as .2's at 350fps)
Can't help but start getting all factual up in here...