You mean query letter, not cover letter. Queries and cover letters are two different things.
Let's call your characters A and B.
Character A = the one the query focuses on
Character B = the one the story actually opens with
Do A and B have about an equal amount of POV scenes? Is either of them "more" the main character than the other? If A is "more" the main character (which is presumably why your query focuses on A), then why doesn't the book open with A? Is there a good narrative reason to open with B instead?
Is the opening with B brief, and do you switch to A quickly? Or are we with B for a while? If B is the focus for a while, and is a protagonist, then the query should probably focus on B. If B is an antagonist, then B should probably be worked into the query.
Without more details it's hard to say, but hopefully this gives you some stuff to think about.
Sorry, of course I meant to say query letter - a slip of the tongue.
In my first chapter, that is about 8 pages long, the first 4 1/2 deal with the attack on the plane with character B. In this part, character A is mentioned several times. The remainder of the chapter (a second scene) deals with character A (alone in her hotel room). While I have not actually counted pages or scenes, I would say that POV is divided about equally between A and B.
The reason I put the first chapter in this order is because I think it is more a exciting scene to begin the story. In reality, the scene with character A sets up some of the overall theme of the story and, in fact, invites charterer B to join her. He's on the plane as a result of her invitation.
Both characters are protagonists. A is an archeologist, who will ultimately uncover a fantastic treasure. Character B, her boyfriend (and soon to be fiance), also happens to be an ex CIA operative. His training and experience is needed to help defend the archaeologist and her group from the antagonists. They are together throughout the story. POV changes through the story to highlight various aspects of the action, not the least of which is the emotional feelings they have for each other. I also use the different POV to expose the different ways they view various situations, people, etc.
By the way, I've post the first chapter in share your work - thrillers.