A big factor in the final could be freshness and preparation.
Madrid have the chance to rest players leading up to the final and basically have weeks to prepare solely for this game. Whereas you expect Liverpool will have to be all in for every game for the rest of the season in the league and FA cup final, hopefully the fatigue sets in at some point.
It's also possible Madrid just have the glow this season, I've never seen a team be this fortunate, it almost feels like they're destined for it ala Chelsea 2012. Although they don't look to be the best team in the competition, they're clearly a side with quality - Vinicius should hopefully give Trent some problems, Benzema's in the form of his life, and when Madrid have needed game-changers to come off the bench they've been able to bring on players who can turn a game around.
Certainly not a given for Liverpool, I'd only have them as slight favourites. My gut feeling though is Madrid get it done.