The two things are probably not related - we have been using Freemake for ages - in an IT dept - with machines that are scanned every day and have on access scanning enabled and Malwarebytes running. In fact we downloaded it last week and it was fine. It does include an option to install some adware - you just have to decline it. You also don't have to install the browser plugins if you are worried about browser security..
Just downloaded it and scanned again (AV and Malwarebytes) and checked running processes - nothing.
Sorry you got a virus but I seriously doubt it had much to do with Freemake..