I always cut out the liner, too, provided I find roomy-enough trunks that I can do that, or that ideally don't have a liner. They weren't provided in trunks when I was younger -- you were expected to wear a swim jock, otherwise your stuff might pop out from one of the short legs those suits had, especially when you sat down. I actually saw that happen on the beach a few times to guys who neglected that extra item under their trunks.
But the longer legs of todays trunks have eliminated the possibility of that wardrobe malfunction, so I find the liner unnecessary, and uncomfortable. Actually I often find the suit itself unnecessary, since I prefer nude beaches, and pools at private gay homes or at gay guest houses. But at public beaches or mixed pool parties I have to keep some trunks handy.