Believe me, I don't get it either. Just one of my personal ick triggers. Probably has something to do with the thought of getting a cushy pad dirty, than a thin pair of underwear, that I can see is clean when they are done being washed.

That said, if I am cycling a few days in a row, it is much easier to just switch underwear than to wash or carry extra cycling shorts. After having switched to compression synthetic boxer briefs, I haven't had any soreness issues up to and including metric centuries doing so, so I really have never had any impetus to change what I am doing.