I always found that once my foot hit the front wheel a few times on a given bike somehow it just stopped happening. I am not sure what I do different, but after a bit of time on the bike I never touch the wheel with my foot, but also never do anything consciously to avoid it. Something in my subconscious just avoids it. I guess that doesn't happen for everyone.
Could it be a matter of degree? Perhaps riders can compensate for, say, a quarter of inch of toe overlap, but not an inch. I did not measure how much toe overlap I had, but in three years of riding the bike, I never acclimatized to it.