What exactly do you mean by home made? You made a complete fan of some kind, or rigged a normal case fan to a usb plug?
The effect it will have on the motherboard depends on what you are doing with it. If you're asking whether plugging it in will fry the board or USB socket, yes it could cause some damage. It depends on what kind of fan it is and how you wired it. If you need to ask about it, then you probably don't have the knowledge needed to attempt something like this and make it work.
Most case fans run on 12 volts while USB operates at 5 volts. Unless you know you have a 5 volt fan from somewhere, and know enough to wire it up correctly, I recommend that you just go buy a fan for your needs.
Most common cause of failure of USB-HUBS on PC or Notebooks is electrical overload. There are instances that notebooks go to reset due to electrical overload on its USB ports. The most common scenario of overload is USB-powered drive and cell phone chargers connected on a single USB port.
THERE IS A LIMIT ON HOW MUCH CURRENT A USB PORT CAN PROVIDE FOR A SPECIFIC LOAD. MAKE SURE YOUR FAN MEET THAT REQUIREMENTS.