Show creators Jerry Seinfeld and Larry David wanted to do a show about Jerry and George being mistaken for a gay couple. They immediately had a problem: the concept could be hysterical, but could also come across as totally homophobic, which they didn't want.
The answer -- the "Not that there's anything wrong with that!" catchphrase -- was a stroke of genius. Not only did that give Seinfeld and Jason Alexander license to fret without looking like bigots, but I'll argue that this catchphrase may have helped promote the tolerance or acceptance of gays and lesbians in America. Which is a Good Thing.