There's a third option besides pre-paying and paying at the counter!

if you belong to the rental company's basic program (eg, Avis Preferred, Hertz Gold Plus, etc), you register the card you want to use with the rental company, and then every time (after the first) that you book a car "pay later" with that rental company, while logged in as a member, the car is auto-billed to the card you registered with them. The only downside is that if, for some reason, you want to change payment cards often, that may be a pain to do. (You may have to visit the counter the first time you register a card to show the card and your ID physically, but it's still auto-billed technically even on that visit>)

This auto-billing doesn't work absolutely everywhere worldwide, but in works at the vast majority of USA airport locations and even some of the foreign ones.

And if you always pay with same card anyway, because it's card that gives you primary collision coverage, then it's wonderful to have it auto-billed, isn't it?

You say you've always done prepay. Well, the funny thing is that I've never done prepay, but I've always used auto-billing except in places it doesn't work (mostly overseas). So just like you, but for a completely different reason, I'm almost never "paying at the counter".

And all the same program that support auto-billing are also the one that let you "skip the counter" in the first place. (If you're skipping the counter, you can't be paying at the counter, can you?)