I have used CF-4-1 since the original EOS-1 film camera of 1989, and using this feature has been 2nd nature to me with each successive 1-series EOS, film or digital. Until the EOS-1D Mark III made its appearance last year.
Combination of the AF-ON and shutter button to make AF works took some time getting used to. Using one for AF automatically cancels out the other but I found out this practise is not feasible in AI Servo AF mode when the main subject remains static and not within any of the 45-point AF sensor mark. Due to this, I activated the C.Fn to have AF activation exclusively on AF-ON button and disabled it from the shutter button.
It also took me quite a while to get used to activating the AF-ON button with my right thumb as it would be closer to the * button and the C.Fn option to switch AF operation with the * button and AF-ON was utilized instead.
However, after having used the EOS 40D for nearly a month, using the AF-ON regularly with my thumb is no longer a hassle. And using the same style on the 1D Mark III is no longer an issue either.