when i first got my 2nd generation AirPods i was surprised to find that they hurt my ears too after a short period of time. i too think my canals are relatively small for the AirPods. i was still able to wear them for 1.5 hours, but they were uncomfortable (just sharing this to provide a relative perspective...it was uncomfortable but not excruciatingly painful). i had the mindset that maybe i would get used to them, else i would pass them on to my wife who found them comfortable.
i was, however, surprised by the experience because my old EarPods fit ok. they weren't super comfortable, but i had hiked 3 hours at a time without noticing any real discomfort. so i pulled them out and i noticed that with the wires, they hung more vertical than i was putting in my Airpods. i adjusted the positioning of the AirPods and found i could make them more comfortable.
since then, i still don't always get the orientation of the AirPods right but usually after some fiddling they are more comfortable. not as comfortable as my Etymotics or Sennheisers which i can wear for hours, but good enough to be comfortable for 1-2 horus at a time. one thing i do try is to not pus them in very far/hard. i at first was worried about them falling out so i was probably subconsciously pushing them in more than was needed. (of course, for folks with larger canals, they should push them in further to ensure they don't run the risk of the AirPods falling out)
anyway, my suggestion is to try fiddling with the positioning of the Airpods. everyone's ears are different. of course for some people, i'm sure they will be uncomfortable regardless of positioning. but for me, i'm probably a borderline case and thankfully can get them in a semi-comfortable position that is acceptable.
