I think it might just be a question of "feel" as a result of your rearsets. The standard footrest comes with quite a strong return spring hooked under the pedal so you feel some resistance when you press it.
When you remove the standard pegs, you lose that spring. A lot of rearsets don't come with a replacement so it's hard to gauge how much pressure you're applying. Some rearsets do have a small conical coil return spring like this one from Sato
http://satoracing.com/brakereturnspring.htm that fits on or in the master cylinder and that can improve the feel.
My current rearsets don't have a spring and I had thought about fitting one but soon got used to the feeling so didn't bother. Now they feel perfectly natural.
Hope that helps.