Consider this passage from the end of the chapter:
They weren’t happy, and neither of them had touched the chicken or the ale—and yet they weren’t unhappy either. There was an unmistakable air of natural intimacy about the picture, and anybody would have said that they were conspiring together.
Tom and Daisy are cut from the same cloth, so to speak. They both want to status and recognition that come from wealth, particularly old wealth. They are fashionable. When Daisy hears of Gatsby's illegal dealings, she begins to doubt him and to be turned off of him. Then, when the accident happens, Daisy and Gatsby are thrown further apart and Tom and Daisy closer together - conspiring together. Also, Daisy herself says earlier in the chapter that she does love Tom. So, faced with two men she loves, she chooses to stay with the one who a) has the respectable money; and b) to whom she is already married. It is the easier path.
Everything comes out in the open in chapter 7, and Gatsby tries to force Daisy to tell Tom that she never loved him. When Tom accuses Gatsby of being a gangster and earning his money dishonestly, Daisy watches and listens, looking at Gatsby with frightened eyes for the first time. She withdraws into herself, unable to say anything. Staying with Tom is the safe thing for Daisy. At worst, her life will continue as it always has been. With Gatsby, she would have to risk too much, and she's not willing to do that. As a result, she reconciles with Tom, especially after she hits Myrtle. She knows Gatsby will protect her, and she just wants to get out of the mess she's created and leave Gatsby to clean it up.