Wow, I have never heard of a ceiling fan cracking the ceiling, but this could be the first.
If indeed this is the cause, I can invision that some one use those tension metal brackets that fit between two joists and you tighten down ont he bolt and this supports the fan and the electrical box. I imagine that if someone really ratcheted down on this product, it could cause the roof joists to actually bow. It sounds very remote, but possible.
Now, IF this is the actual cause, you can do this if you want or just leave it. I doubt that it will grow on you though.
I would remove the fan from the ceiling and then remove the electrical box after YOU HAVE TURNED OFF THE ELECTRICITY then loosed the bolt acouple of turns so that it is not so tight and not too lose either. Then re assemble the fan. Now the question is if the rafters will seek their original position. I doubt they will since they may be comfortable in their new position.
Then you could not do this and just force in latex caulk into the crack and let it dry and paint the area. Caulking would be flexible. You could use spackling, shrink free also, but it is not flexible.
Are there any cracks around the tops of your doors in any rooms? Do all your doors and windows work properly? Do you have any cracks on the exterior walls of your home? Do your have big cracks in your soil around your foundation?