well, the most obvious answer is that it gives your opponents more Free Throw attempts. If you go against a team that as very good free throw capabilites you will have lowered chance to win.
a broader question, that I do not have the answer to, is HOW can you get your players to have fewer fouls?
my guess is that if you play a Zone defense then your team would probably have fewer fouls. also another GUESS is to not press, as pressing players may tend to foul more. (but these are just guesses)