I guess I'm a bit biased, since I thought Brosnahan gave a really strong, extremely nomination-worthy performance - but even if I try to put aside my bias: let's not forget how thin this category is right now.
Laura Linney is an unknown quantity - she's a terrific actor, but we don't know what the role will look like, or whether the play will be well-received. And as for Audra: she's always great in everything she does, but Tony nominators have already shown once that they're willing to pass her up for other people if they feel like it, and Ohio State Murders wasn't well-liked (or maybe it was, by the nominators specifically, but we won't know until we know).
I'm not saying it'll definitely happen - but with a race like this, all it takes is a little wobble for one of the others, and Brosnahan is right there to take their slot.
Another possibility: both Laura Linney and Jessica Hecht are categorized as leads, AND the Thanksgiving Play actors are considered leads. Then we have 9 actors eligible, making it an automatic 5 nominees. Then Brosnahan would technically have more competition, but if she's a stronger candidate than Hecht, Finneran, and Carden, then it's a totally viable path to a nomination that wouldn't involve kicking out Audra or Linney.