I have use Fritzing for years now, and love it. I have managed to produce several PCBs, and have noted that the vias are always uncovered with the solder mask. That was never a problem but now it is because, it is creating a contact with an external component in my device.
Can Frizing allow adding soldermask to vias?.
or
is there a tool to add solder mask on specific regions of the pcb?
I was getting tired of repeating the steps above after every little change I made to my files so I decided to see if I could modify Fritzing to export gerbers with the vias tented. It turned out to be a trivial change. I have created a branch with tented vias. https://github.com/Intrinsically-Sublime/fritzing-app/tree/Tented_Vias
To use it you would have to compile the source so it is not as easy as downloading and for most people the steps in my post above will likely be easier. I will make a pull request to to the main repo but it may not be excepted and even if it does get excepted it may be a long time before we get a binary release.