Yeah, that's the thing... this "under 50% chance of winning" thing doesn't make sense. If she runs, there's basically a 95% chance she's the Democratic nominee. If you give her a 65% chance of beating the Republican, she's the odds-on favourite.
This is the heart of it. It's not that Hillary is a "perfect candidate" (and certainly not my personal perfect candidate) but the Republican brand and bench for 2016 looks terrible. When the one party is going to find it virtually impossible to find a nominee who doesn't present as a bigoted, anti-science, corporate stooge without their party splintering, then the alternative does indeed look like a shoe-in.
Generic Republican could beat Hillary. I just don't see the scenarios where Actual Republican does, even though, on paper, this should be a great year for the Republicans.