I hope I'm not entering a minefield here... but from what I've heard, it sounds like he's not against vaccines in principle, just ones that haven't undergone clinical trials equivalent to what the FDA requires for pharmaceuticals.
(A sound byte I heard sums it up, where he said something like "no one called me anti-fish for working to get mercury removed from the fish sold in supermarkets, so I don't see why I should be labeled 'anti-vaccine' either.")