A good fraction of the time, the official site actually links to Download.com (or some other download site) instead of providing the link directly. For example: Irfanview (http://www.irfanview.com/) is a very good/popular image viewer/editor for Windows. If you go to their download page, they provide links to their software installer on Download.com, TUCOWS, and half a dozen other sites).
I expect this is mostly done to cut the site hosting costs for the main site. If everyone downloaded it directly, that's a significant bandwidth bill - but by farming it out to a number of other download sites, those sites pay for the bandwidth. This also lets the you leverage regional mirroring, again saving bandwidth costs.
So - it's a common thing.
People are aware of the issue with unofficial download site, which is why Download.com and others often advertise "trojan/spyware/crapware free" or some variation of that.
And up until recently, I've never had any trouble with these sites. I do recall the change when Download.com switched to the silly installer a few months ago (August time frame I think) - I just selected a different download mirror.
Download.com is now officially on my DO NOT GO THERE list...