I wear running short with liners, and I usually do wear underwear - I'm with Pika, I don't wash them everytime I wear them, so . . . undewear are probably a good idea. I run 5-6 times a week and only have 2 pairs of shorts I like, so they get lots of use.

But my favorites are a size too big (that's why they're my favorites!), and as I was running today, and the liner was bunching and the cotton undies were bunching a bit . . . I realized I would probably be more comfortable without. But old habits die hard.

I don't think the only purpose of the liners are underwear-substitutes - they also keep the shorts from riding up.