I think the big reason for this is the fact that many altcoins and tokens are very shady and the people behind them often engage in market manipulation via pump and dump, so they can afford to pay those fees, since they will still be in profit. This is harmful for honest projects since their developers have much less funds and can't afford listing.
I wonder what the landscape would look like if this wasn't a thing.
Exchanges would try to list coins basing on their popularity, to make sure that they get the most fees. Some coins might be unprofitable to list, because of very low volumes.