I am required to wear attire that covers up my private parts, does this mean I am oppressed too? Or is it just that other cultures have retained different standards of modesty from us?

Your point about applying the same standards to all belief systems sounds great on paper but its the reason your philosophy does not work. Belief systems evolved from different cultures and at different times. You cannot apply one universal standard to judge them all. What is seen as oppressive by us may be liberating to them, and vice versa. For example, a society that requires its women to get educated and compete with men in the marketplace can be seen as oppressive by a society that has placed such a great importance on women's happiness that only men should work so that they can supply their women with everything they could ever need and want. You can't judge other societies by the standards we hold, our standards are different. So what we do is take a step back and say ok, believe in what you believe as long as you don't commit crimes. Once a crime is committed we can step in, and that's perfectly ok.

How does protecting freedom of religion mean we are not protecting "primary qualities such as gender and skin color?"

How can freedom of religion "fail?" Either we uphold the freedom because we view it as important, or we do not uphold the freedom and let it fall. What this freedom means is this: if there are 100 Muslims in Canada and 99 of them choose to become terrorists tomorrow, we have absolutely no authority to make the last one change his religious beliefs because of our views on his religion. I agree with this 100%. Individuals should be judged on their actions, not their beliefs, and I will lay my life down to protect that last Muslim person because it is no crime to practice a religion. People are innocent until proven guilty.