This might be simplistic, but I think one reason is that women are smaller than men, on average. Women rarely have ruled in civilizations around the world because they were smaller. (How many great pygmy empires have their been?) With being smaller comes oppression. If women were the same size and strength, on average, I think civilization would be much different. I read an article a few years ago on various animal species. The ones in which males and females were the same size were monogamous; the ones with a huge difference in size were typically polygamous; humans are near the same size but women are a bit smaller and humans are considered by some scientists to be "predominately" monogamous. Some species, like black widow spiders, have substantially larger females than males, and well, suffice it to say they are polygamous.
As for your specific questions, wow, those are some good ones. I hope some of our forum members have some good answers. I'll take a crack at a couple..
-"So here are my questions, why do we think this way? -- Millennia of oppression (see above)
-"Why is a mans natural face fine but a woman must mask hers in layers of make up?" -- For much of history, men have obtained as beautiful a wife as his wealth could afford him and women have obtained as rich a man as their beauty could afford them. I don't like this either, but it appears to be true much of the time, as women have necessarily depended on the wealth of men for much of history.
Fortunately, in parts of the world, especially parts of western civilization, the concept of gender equality has taken hold (especially in places like Scandinavia), and women have gained more rights. It's changing, but reversing a long history is taking a while, longer than most of us think it should be.