First, there is some evidence that Muslims originally prayed toward Jerusalem, not Mecca. Second, you can play the same game with Christianity and Judaism. I can point you to any number of atheist web sites that list dozens of peculiar things about passages in the Bible. What's a Nephelim, for example? Third, do some reading concerning Biblical archaeology. They've found statue pairs of Yahweh (God) with a Consort (goddess) in digs in Israel. There is evidence of pagan influences on Biblican stories. The same sorts of claims about the origins of buildings and practices have been made about Judaism and Christianity. Just tune into any Creationist vs. Evolutionist thread on Free Republic to see how many people, even here, think the Bible is full of hokum.
Ultimately, these are all legitimate complaints and issues to raise concerning Islam. But they have almost nothing to do with the point of this thread, which concerns whether Muslims can be good patriotic Americans.