I don't think she ever was a "shoo-in." Marissa has been giving her a run for her money. Obviously I am routing for Bernadette, but I'm not going to start a message board protest or start ranting like a lunatic if Marissa wins.
My whole theory is that the Tony's are very political (much like the Oscars). They may give it to Bernadette because, mixed reviews or not, she does a phenominal job in Gypsy; and she has made reference that it may be her last Broadway show (yeah, and Barbra's really finished with concerts).
As much as the voters do like new-comers, they gave it to a new-comer (Sutton Foster) last year....though she clearly deserved it. They may go for the veteran vote this year...but I think Bernadette and Marissa are both very deserving.
"It's the little things; the details, that distinguish the Barbra Streisands from the Rosalyn Kinds."~Gilmore Girls~