More often than not, Endora didn’t approve of her daughter’s marriage with a simple human because of one thing: her daughter shouldn’t hide herself and her true powers, because that meant losing her freedom.
But Samantha was well aware of this, and she truly wanted to lead a “normal” life, as a suburban housewife. She already lived the life of a witch, so all she wanted at that moment was the life of a “normal” woman. And Darrin surely made this a point when forbidding her to use her powers any longer.
But Samantha’s powers aren’t just the magical ones. She is intelligent, she has wit and quite a lot of it, since at times Darrin feels threatened about this also. It isn’t a fear for his own life, but rather a sexist fear concerning the role of a woman in a marriage: to serve her man.
Bewitched may be considered the first television series in which an actual superheroine is depicted (while, at the same time, being also the first show when such a character surrenders unconditionally). But this is also a series in which a statement is made concerning the role a woman was needed/was forced to assume when becoming a wife.
And this surrender doesn’t concern just the social aspect of being a spouse. Darrin felt threatened in his position as the head of the family even when they were all alone in the house. Thus, she became entrapped completely, since she had to renounce everything that could have helped her if she was alone. In other words, Darrin was trying to make himself indispensable.
As said in the show, a woman’s job was exactly this one: I mean you’re going to have to learn to be a suburban housewife. [. . .] You’ll have to learn to cook, and keep house, and go to my mother’s house for dinner every Friday night.
I believe that this was the underlying statement made by the show: Bewitched was trying to speak out about a woman’s rights (or lack of them) as an equal of the man.
So why did Samantha enter a marriage with Darrin and remained with him until the end?
As said, she was very intelligent. And, as an intelligent person (I am using this word in order to transcend the barriers set by the genres) she decided that she wanted to live with a human, even if that meant clipping her own wings.
But then again, like with plenty of other shows, the comedy is born from these types of situations. It is all about the satire. It is all about saying that when you try to impose your supposed superiority on another human being you will end up looking like a fool (and, who knows, maybe you will too be switched, just like Darrin was).