I have not seen two of the nominees yet, so I will not comment on whether he does or does not deserve it vs. some other nominee.
Re Tootsie, as time goes by, I find myself disliking it more and more, my disinterest driven by the awful score. Because of that. I would rather have seen it as a straight play.
I thought Fontana was fine in the role -- probably could not have been better, given what he had to work ,i.e., bad music, unimaginative direction, choreography constrained by the limitations the music. I think the lack of good musical material limited his performance; and, as a result, I don't think he would be a sure thing in a season with better musicals.
Looking back over the last decade, were the show presented in any of those seasons, I think I would have voted for him maybe once: in 2015 (I hated Fun Home and am not a homophobe).