The fundamental issue I have with him is that his "liberal" approach is skin deep only.
His double standards when it comes to Islam and then his quasi intellectualism.
His Zayatuna Institute and the way it is run resembles a cult - at least this was my impression.
He's like a rock star for the Muslims.
Look into the eyes of the women veiled in black in the video you have provided, study her facial expression.
Also some of his debates with atheist/agnostics and responses he provided were unworthy of a true intellectual.
Have you ever seen/heard any of these quasi intellectuals condemn Islamic colonialism or Islamic slavery for example?
They are always quick to condemn Western imperialism and they tend to blame it for the misfortunes of Muslims. How come ALL imperialisms aren't equally condemned by those guys?
Have you seen this:
http://www.youtube.com/watch?v=n-9-oBTuwfwSign of a truly smart individual is to know when to keep one's mouth shut.
Here is what Richard Dawkins had to say regarding the video:
"It is very clear that he has not read any books by Sam or by me. I suspect that he is confusing TGD with the documentary Root of All Evil. Most probably he has not seen ROAE itself, but read a review of it. 'Picks on the worst of religion' was the commonest criticism of ROAE, and it frequently went with something like 'How would you like it if people judged science by picking on the worst examples of science?' I don't think anybody said that ROAE picked out the best examples of science, because it wasn't, after all, about science. But it would be easy for this idiot to misread the 'How would you like it if . . .' line in the way that he apparently has, assume that the film did that very thing, and then muddle the film with the book.
He is an American (real name Mark Hanson) who converted to Islam and took a fake Islamic name. Sounds more impressive doesn't it, Shaykh Hamza Yusuf, than Mark Hanson? Does any psychologist or sociologist know if it is a standard thing people do, if they are too inadequate to make a success of themselves in their own culture -- change your identity and re-invent yourself, to see if people take you more seriously? It is very believable that somebody as palpably stupid as this would not make a name for himself as an ordinary American called Mark Hanson. But as Shaykh Hamza Yusuf, The Guardian describes him as "arguably the west's most influential Islamic scholar" and he is said to advise Bush on Islamic matters."
On a side note I find the fact that a veiled woman (and I mean this in a strict Islamic interpretation) considers herself to be a champion of human rights and establishes a shelter for the victims of domestic abuse truly ironic.