I find his comments and positions on LGBT issues disconcerting at best, though I'm unsure he qualifies as homophobic. He seems to have turned a corner on LGBT issues from what I've read.
OTOH its less politically acceptable to be homophobic now so who knows whether this chnge of heart is born out of expediency or not.
But I do think he's eminently qualified, in particular I appreciate his measures positions on Iran and Israel and the fact that he served, which lends him perspective on the consequences of his decisions. Perspective people like Runsfeld lacked.