If it's free and it isn't clear how they make money, then YOU are how they make money. This site is most likely selling your information, injecting adware/malware/spyware into your downloads, etc. I wouldn't use it.
People are making a big deal out of MacUpdate's installer right now, and it's mostly overblown "Internet rage." Create a free account and log-in to MacUpdate and you won't get the MUDesktop installer when clicking download on your favorite app. Problem solved.
MU has been providing a fantastic service for free for a really long time. They make it clear how they're making money, they don't try to hide it, they make it easy to "opt out" of taking part in it. I'm not sure what else you can ask for from them if you're not willing to pay a monthly fee to avoid all of it. And we all know nobody is going to pay a monthly fee, so let's not pretend we would if it were only available as an option.