This was one of the things that always confused me about the levels in the Megaman games. Why did Mega Man always have to start at the beginning of the levels? Why not have Mega Man beam directly into the Robot Master's lair? Why risk his destruction by having him fight all those robotic minions on the way to the Robot Master's lair?
Having thought about this, I've come up with several possibilities. One of which is that perhaps the Robot Masters' lairs and the immediate vicinities are protected by some sort of anti-teleportation shielding... but that wouldn't explain why Mega Man could beam in after he dies or why he could beam out after he's defeated the Robot Master. In fact, how could Rush beam in when he's called? Well, unless Mega Man is somehow able to disable the shielding as he explores, meaning he's able to teleport it only to areas he's already explored...
Or maybe Dr. Light can't beam Mega Man directly to the Robot Master's lair because doesn't know exactly where it is. He can beam Mega Man to the general area, and then Mega Man has to scout around for the lair. But that wouldn't explain why you'd have to beam back to the beginning of a level if you revisit it later, would it?
Then again, maybe Dr. Light can't scan the areas surrounding the Robot Masters' lairs, due to a jamming signal or something, and is worried that if he attempts to teleport Mega Man without knowing the terrain, Mega Man might materialize inside a wall. But he can track Mega Man as he travels, so he's able to teleport Mega Man in to the same area if he dies and teleport Rush in near Mega Man when called. Though, I know I've accidentally beamed Rush into a wall or two in my day, so maybe that's not it either.