Anymore you need to for most FPSes to know what you're trying to do. Doesn't mean I don't gloss over the details if it's a particularly crappy plotline. Red Faction, while a truly satisfying gameplay experience, had a plotline that I only paid attention to when someone said "okay, you need to...." Doom 3's plotline was easy enough to grasp, didn't require much thinking. And Half-Life 2... one of the reasons that game pisses me off so much is that they have this reasonably decent plotline with absolutely no f%$#ing explanation for anything. Hopefully the expansions that will no doubt come out for it will clear up some of that.
Then again there are games where you don't even know the plotline if you didn't read the manual. Like FarCry. The first half of that game I was going, "wait, why are they trying to kill me again?" It was still fun and visually stunning... in fact I think I may go play it again now.
Oh yeah, Serious Sam. Plot? What plot? Kill things you idiot. Love those games.
P.S. Deus Ex is one you really needed to pay attention to. Of course that's more like a FPS-RPG. Too bad Invisible War sucked donkey balls.