An interesting topic and I fully agree that if you always use autobrake and never brake yourself you may be a bit rusty when you have to for some reason. I think it is like other problems arising from overuse of automation, you need to be familiar with all modes of operation and vary your game.
There are plenty of arguments in the other direction. Indeed I think part of the overrun problem in Chicago with Southwest was that the pilots were not familiar with the autobrake system. The brake to vacate concept is also on its way at least with airbus. I have certainly heard that the automatics are softer on brakewear when used properly.
As an aside as a sim instructor I find people tend to be a lot less smooth manouevering on the ground in the sim than in the aircraft, perhaps due to sim fidelity problems and lack of cues that are available in the real aircraft.