I'm not sure why they tried: all signs prior to Kerry's announcement from Davos were that a filibuster would fail miserably, so why did they try? Neither of them are in any danger of losing their seats as a result of the filibuster, of course, but how does it make political sense to start a doomed battle? I find it hard to believe they're that principled.
The only explanation I can think of is money: they can tell MoveOn.org that they really tried to stop Alito, but avoid fallout from centrist voters concerned about Democratic obstruction. But Kerry still has plenty of money from his presidential run, last I heard, so does he really need it? Ditto for Kennedy.
Or are they really just that incompetent?