(Around the same time he did a pretty cool soundtrack for a grade-Z Western with Mercedes McCambridge, I forget the title.)
Oh Phooey, Tom is just as stridently anti-Zappa as anyone else here, and has certainly been talking about it longer--see the 7/3/01 show, where he challenges listeners to "name one Frank Zappa song that doesn't suck." Being funnier than us doesn't make him less uncompromising. And he does sometimes hold an artist's fans against him or her (see Waits, Tom).
(I admit I don't really know what Tom had in mind by calling him "conservative," but the strident part of me thinks any anti-Zappaism is good anti-Zappaism.)