I too have experienced the same issue with my left thumb, and it aches terribly during my journey. I've found that re-positioning my hand and applying less pressure on the button often helps.
I used to seem to start off by peddaling, then pressing the button hard, thinking that I should be pressing it firmly, yet when I press it gently, it's (obviously) no different. So, I now try to make an effort not to press it too hard and this often saves 'thumb strain'.
My button sits quite close to the rubber covering, and ergonomically, it appears to be in the most suitable location.
Just looking forward to an evening's outing tonight on it. Went out in the rain the other night, and it wasn't very pleasant, so will try this evening if I can.