If you are writing a novel, then it is assumed that you understand the basics of how to put a story together. You comprehend, at least on some level, the three-part story arc and how your words are supposed to follow that path. The thought of writing a 300-page story full of twists, turns and (hopefully!) lots of action doesn't scare you that much. However, if you are asked to write a three or four paragraph query letter and you start sweating worse than a Biggest Loser contestant on week one and break out in hives.
Why is it that people who craft intricate stories that thrill the masses become Dom from There's Something About Mary when it's time to start that query? Here's a better question: why is it that agents and publishers who are looking to see if we would-be authors can turn a yarn that people will want to buy do so by seeing if we can write something that is the literary equivilant of Hot Wheel sitting next to an Imperial Star Destroyer?
Go to any agent blog on the web today, and there are thousands of them, most really well done. Do a search and I will bet you my empty Germ-X container that the most written about topic is query letters and how to write them. I find that interesting, because these agents are looking not for good three-paragraph stories, but rather 300-page stories. If anyone were to ask an agent why they do it this way, I'm sure that the response would be something close to "it's the most effcient way to tell if a story is marketable." And they would be right. They know more about their business than anyone who's not in it. But, surely some smart person can come up with a better way of doing this than something that all writers, and most agents, dread worse than life itself.