I'm still unsure about how to proceed with Tariq Ramadan. His visa was approved by the State department, but then denied according the U.S. Patriot Act, presumably the "public supporter of terrorism" clause (though DHS refuses to say). He has not been accused of actually being a terrorist, nor is he under suspicion by any American or international agency. He has been accused of being anti-Semitic for condemning French Jewish intellectuals who support Israel.
My first instinct is to doubt the U.S. government's motives and methods in denying him the visa. Since it is probably his public actions that are at issue in their decision to deny him a visa, perhaps the merits of the U.S. government's decision might be worked out through a close look at Ramadan in the public record. As for his private actions and connections, I'm not in a position to know or say. Nevertheless, many specific charges have been made against him in public by journalists (especially a French journalist named Brisard), and I have a suspicion that these played more than a small part in the DHS decision to deny him a visa.
Scott Martens has done the most exhaustive research into Ramadan I have seen on the web. In the link above, he sets up the basics of who Ramadan is and why his visa has been denied.
But here, Martens goes into some depth, and reads in detail several articles published only in French to refute charges made against Tariq Ramadan by Daniel Pipes. There are dozens of strange charges that have been made, including statements made by people detained in Guantanamo on suspicion of being terrorists that they had taken classes with him (which actually turns out to be impossible chronologically). Other charges include: reports of meetings with terrorists (people Ramadan says he's never met), and mystery bank accounts (also denied).
There are lots and lots of details -- too many details for me to be quite confident in making a general judgment yet. Many of the articles cited by Pipes, Martens shows, are dubious -- or they don't say what Pipes says they say. At the end, much of the suspicion of Ramadan seems to circulate around him because his grandfather founded the Muslim Brotherhood (originally as a reformist movement; it became associated with terrorism more recently), and his father and brother are Islamists.
On the question of whether Ramadan is anti-Semitic, I don't buy it. He published an article in French that was published here, where he criticizes French Jewish intellectuals. Angry, yes. Anti-Semitic, no. There is more on this at Muslim Wake Up!; especially helpful is their link to this interview at Ha'aretz.
Closer to home, there is also an excellent colloquy (live on the web) with him sponsored by The Chronicle of Higher Education. He comes across well.