The NFL has rules to try make this ineffective: for one, taking two delay of game penalties in a row is an unsportsmanlike conduct penalty. There's also various rules that try to eliminate strategic use of penalties to run down the clock by making the clock stop on penalties at the ends of the halves.

You still see delay of game penalties by teams running down the clock fairly regularly, but it's more to just use every available second of the play clock up, typically in a situation where the distance loss isn't very important (like right before a punt).

Furthermore, sometimes you want to lose the distance so that the punter doesn't have to struggle with a punt that's on the short end of his comfortable range.