Why would someone who has a 99% chance of winning the nomination and a 50% chance (at worst) of winning the general not run? Unless they really don't want to be president, which we already know isn't a problem for Hillary.
Because she's been in the extremely high stress position of the national political spotlight for over 20 years consecutively and is too tired for another grueling 10 years of campaigns and governing, by the end of which she'll be nearly 80.
Because she doesn't want her grandchild to grow up with scurrilous accusations on her character like people saying she's a witch and she killed Vince Foster, etc. Because she's sick of such things herself.
Because no matter what she does the press will always treat her every move as a political calculation and will never admit that she has genuine opinions and hopes for this country, like a normal human being.
Because she's actually an incredibly smart woman who understands that just because she seems inevitable today, that doesn't mean anything come a year and a half from now.
Because she's been demonized, vilified, slandered, misunderstood, humiliated, cheated on, condescended to, and erased, and she just doesn't give that much of a crap anymore.
Because she doesn't owe anybody anything, including her "supporters" and hacks and other people in the Democratic party who want her to run for their own selfish interests.
Because she too shares the desire for a new generation to step up.
Any of those reasons might be a reason.