I wear cycling undershorts, with a pad in them, that go under regular shorts. Andiamo & Pearl Izumi are the brands that I use. Both were fairly inexpensive. I think that Andiamo ones have a buy x, get 1 free offer on their website (They did last time I checked). I bought them all last year & have worn them for 1 and a half years now & they all are still in great shape.

Any shorts with a liner are a bad choice for commuting. the liner works like a cheese grater.