In The Great Gatsby, Tom is presented in a negative way. First, though, remember that the narrator is the one characterizing Tom, and he doesn't like Tom. This is clear from the first time he describes Tom in chapter one, when he reveals what he expected Tom to be like before he met him during the course of the novel's story. Nick knew Tom in college, and though the novel's story occurs years later, Nick carries over his dislike for Tom from his college days. Daisy does at least indirectly reveal some of Tom's negative personality traits, but even her words and actions are filtered through the the narrator, since he is the one writing them down. And Nick is not necessarily a reliable narrator.
This is not to say that Tom isn't somewhat as Nick portrays him. He probably is. But in terms of Daisy staying with him this is not a central issue. She doesn't decide to stay with him because he is or isn't a good guy.
Daisy stays with Tom because he is the status quo. Economically and socially, Tom represents old money, inherited money. Tom is on the top of the food chain, so to speak. He is of the elite class. Daisy must stay with him to maintain the status quo. Gatsby is wealthy, too, of course, but he is an upstart. His money is new. He does not have a respectable family name, etc. His family is not well established.
Specifically, though, Daisy might have been talked into leaving Tom for Gatsby, except that, as she says, Gatsby demands too much. Gatsby insists that Daisy make an announcement that she never loved Tom and that even when she married Tom, she was really pining for Gatsby. And Daisy won't lie--at least not about this. She did love Tom once, and she won't deny that. In short, Gatsby sees the relationship they had five years earlier as special and poignant, as something earth shattering, but Daisy doesn't. Gatsby was just one suitor among many, apparently.
Daisy stays with Tom, then, to maintain the status quo and because Gatsby asks too much of her.