Teddy Roosevelt bothers the bejeebers out of me.
Exceptionally effective as President, but I think he really helped drive the future of US politics in Latin America, which isn't pretty stuff. It's not fair to judge his Presidency by it, but he was also one of the strong voices for imperialism. He just seems cocky, too. If he were President today I think I would be scared for the world. Doesn't make him worst, but I hate seeing him lined up as one of the best so often.
@0's: FDR is controversial, many think he set the US back decades or more but was loved for it.
Bosk1 said the best answer, avoid the question. It's easy to find problems with almost any of them, and many of them get crap they don't deserve. The worst ones might even be the ones nobody mentions, corruption has been rampant in many administrations. Look at the ineptitude leading up to the Civil War, look at Manifest Destiny and all the expansionist wars we were in, stuff we glorify from hundreds of years ago would be seen as disgusting in today's Presidents.