Paint.NET became irrelevant when it became closed source. These awful malware buttons are just another example of the same mentality that led to changing the license.
Wait, Paint.net is closed source, and the website knowingly has malware buttons? That makes me extremely hesitant to use the app anymore. If they're unscrupulous about putting those buttons on the website, who's to say they aren't putting actual malware inside the app?
Someone was taking the Paint.Net source, bundling with OSS plugins and replacing all the names/copyright as another piece of software. The person doing so is in another country from the author, so the author decided to close the source.
If you're on Linux or Mac, there's a recreation after Paint.Net called Pinta. It's passable on windows and mac, but the linux version has been very buggy for me, it doesn't seem to be well maintained either. Which is a shame.
I really do like Paint.net a lot, but as GP mentions, actually getting a novice through the download process is scary to say the least.
The last open source release was in 2009, and I recall there being some weirdness with the code being open, but the icons other resources weren't. There where a couple of forks around years ago, but non of them went anywhere.