Who's running the show?

Okay, after several false starts, I'm pretty sure I actually have a coherent plot, or at least enough to get started. I know the who, where, most of the what, polishing the why, and writing the how. But here's the dilema, and it's a doozy to me. My main antagonist, who's in the background a lot and doesn't become a focus until the later part of the novel (though he does make the occasional appearence), is the one who's really moving the plot for at least half the novel. While the protagonist has his goals and is trying to work towards them, much of what he ends up doing is reacting to the villains decisions and actions, and he doesn't even know someone's specifically targeting him yet (as it's not obvious and there's no real connection between the events, save one). It isn't until later that he realizes that, and he gets proactive on that front because he knows it's "me or him". While there are other elements, with his initial motivation and goals and the obvious things standing in his way, it's the background decisions of the antagonist that have the most direct influences on where the story inevitably ends. I'm just a little worried on the fact that for at least half the novel, the main character is in a mostly reactionary position, except for his own personal quest that has nothing to do with the antagonist. It makes sense for the plot, but I'm afraid it might frustrate readers. Is this something I should look into further, or am I just paranoid and worrying too much?

Your main character does seem to be in a reactionary position. The antagonist may have the upper hand to start with, but you need to make the protagonist aware of his motivations as quickly as possible so he can attempt to defeat him.

Having said that, you could make the villain the protagonist. But whatever you do, ensure there is conflict right from the outset and that you escalate this conflict to such a degree that the tension becomes absolutely unbearable, forcing your readers to stay with the story right until the end.

I wouldn't be a good person to give advice here, but all I can say is that as a reader, if I'm beginning to get frustrated because things aren't working out how I expected or wanted them to, then the writer's doing a good job. Now, I don't know what kind of situation you're talking about here, so that might now even apply at all. If you're concerned the reader will loose interest, why not throw a red herring in there? Have the protagonist become suspicious of someone else to keep the readers on their toes.