I have a honeywell thermostat its program to shut down at 530am. The heat shuts off but the fan keeps running. The only way to shut it off is at the breaker panel. Is my thermostat bad?

Did you already checked that the option FAN in your th is at AUTO position? In is not just switch to auto. Depending the kind of furnace you have can be some others problems concerning the fan control system. Some times electronic, electric or just mechanic. So After yoy chec your th. Send more info about the furnace. Brand, model etc.

There is a fan limit switch/cam stat on gas furnaces. They control when the fan shuts off and when it turns on and also the temp limit it can keep the burners on till. Go to youtube.com and look for videos for this and there are many so you can see what I am talking about. You may just have to adjust the kick off setting to higher temp. Let me know if this helps.