Hi Cindy, great question!
I would say tough time is more when you are going through something and you keep going or you are struggling through something. I would say this is more within your control. E.g. I'm completing this problem but I'm having a tough time figuring out the answer.
For rough time, this would be more difficult time that is probably more beyond your control. For example, he's out of luck, he's had a rough time.