Habit, mostly. I also have several hundred dollars of pre-tax transit money on my Clipper card from when I had that benefit at a previous job (and set the paycheck deduction way higher than I should have at the time), and I still haven't used it up. I assume there's rightly no way to get cash back for this, since then I could keep the tax deduction and spend it on anything. (And even if I could get the cash back, likely it wouldn't be worth the hassle vs. just continuing to use the Clipper card. The card is on my phone, so it's not like the experience would be any different.)

Also I don't mind saving SFMTA a bit on transaction fees. I'm sure the total transaction fees are lower with me periodically topping up my Clipper card, than if I used a credit card for every ride. I expect me doing this is probably only saving a few dollars per year at most, but it makes me feel good to support my local transit authority even in a tiny way like that.