I wouldn't say it is obvious. The ads you got when you took your screenshots weren't the most confusing that show up. Here is what I got on the site:
http://imgur.com/a/WvFd6First impression for me of the page is that the content is on the left, and the ads are on the right. That's because the part I have circled in red looks like Google-style text ads. My mental ad blocker filters them out.
The download button I have circled in yellow then sets off alarms. It's in what I have decided is an ad column, and the color reminds me a bit of the deceptive download ads CNET's download.com likes to use on their site to trick people into downloading the wrong thing.
I return to the left column, which I have identified as the content column. The download button there, which I have circled in green, is in a place where a download button would not be unexpected. This is the one I will probably click, unless the small, greyed out, notice that it is an add for "Free Zip" somehow catches my attention.
If instead of trying to download from the front page, I click the download link at the top, we get to the second page. What I'd do there depends on how tall my browser window is. If it is tall enough to show the real download section at the bottom, my attention would be drawn to that, because it looks enough like download sections at other places (because of the layout, and because it lists versions, sizes, and mirrors).
However, if that ends up not visible, then I'd probably click the ad I have circled in green. This ad fits right into the flow of the content and is a place where a download link for paint.net would make sense.
I think pages can be classified into "consumption" pages and "activity" pages. A consumption page is a page where the reader is there to consume the content of the page. For example, a product page at an online store would be a consumption page. The reader is there to read the information about the product. The front page of the paint.net site is a consumption page.
An activity page is a page where you are there to perform some activity. At an online store, the checkout page would be an activity page. At the paint.net site, the download page would be an activity page.
Third party ads on consumption pages can be fine. People on consumption pages are often just looking, and ads give a chance to get some money from such visits. When people get to activity pages, they have usually gone beyond the just looking stage. You've got them on the hook, and now you want to reel them in. There should be no outside temptations or distractions put up at that point.