Is it safe?

From FaHWiki

The Folding@home client and distributed computing service is no less safe than other programs that you can download from the internet and run on your computer. Because security of the FAH client is very important to the Pande Group, they have designed the FAH to be as secure as feasible through encrypted downloads/uploads, file checksums, etc. FAH should not reduce the security of your computer.

Reference Links

• Running the console as a restricted service
• Folding-community: Security issues