That a fair bit of the world's workings can already be explained by science. Eg. evolution, the big bang theory. We might not know everything yet but that doesn't necessarily mean that it's magic or spiritual.
That nature doesn't comply to morals. Animals eat each other alive, kill for sport, thieve. Why would God's laws and morals only apply to the human race?
There are lots of different religions and Gods. Some of whom are very unwilling to share the limelight. How do we determine which one is the REAL one? Isn't it just as likely that none of them exist?
That religion makes a lot more sense as a manmade construction (to reinforce law and order, as a teaching tool, as a bunch of stories trying to make sense of the world) rather than a fundamental truth.
That religions bend according to the era (to an extent.) As I see it- religions are businesses- if their laws become TOO strict in a more liberal era- people start to turn their backs on religion. So to draw the people back- those laws become watered down to be less restrictive. If religious laws REALLY were so absolutely the word of God- no mortal would be able to change them.
That all said- I'm not an outright unbeliever (although I would like to be...) I think if there is indeed a God or Gods or a higher power- we're all in trouble because- looking around, I think they are a sadist...