Writers groan when they hear this, but I can understand both sides. The quality of a query can oftentimes be a good indicator of a writer's grammar, spelling, and sentence structure. It's also an example of the writer's style and their ability to summarize information--too much back story, not enough conflict or voice. All of this can be true of the manuscript as well.
But not always! When I read the entries for the GUTGAA agent pitch contest, there were a lot of queries that were either too long, too short, repetitive, or didn't present enough information (character, conflict, stakes, what makes it unique). If I was an agent with nothing but the query to go on, I would have passed on them. But then I jumped down to the first 150 words, and they were solidly written with a great voice that drew me in, and I would have definitely kept reading.
Sometimes, no matter how skilled a writer you are, writing a good query is just REALLY FRACKING HARD. And because agents judge whether or not they want to read your book nearly entirely on your query, this can really suck.
Unfortunately, you can't just say 'oh well' and cross your fingers that the agent will request based on the sample pages alone. Well, actually, yes, you can, but do you really want to? It's true that some agents have said they skip right to the pages to see if it draws them in, but even more agents never make it to the sample pages because the query didn't do its job.
When an agent says they pass because they fear weaknesses in the query will reflect weaknesses in the manuscript, it's because they've read a LOT of queries and pages and generally know this to be true. But the thing is, sometimes--a LOT of the times--it's not, and the agent won't know that because they just don't have the time to check every single query.
So while, as a writer, I think query-writing can arguably be a form of torture, the unfortunate fact remains that it doesn't matter whether or not the quality of your query reflects the quality of your manuscript. No matter what, you have to put your best foot forward and prove that your manuscript is worth the read by proving it first in your query.
And yes, again, that's REALLY FRACKING HARD, and no, there's no single right way to do it, but I know you can! You wrote a whole book, after all. That already means you rock.
Good luck! ♥
and my utter inability to draw a guitar *wince*