I pinged someone I know, and they responded with the same FAQ page, pointing to number 1, the ads.

From what I understand, the uploader can specify if they want ads added to the video to then get part of the revenue generated. These videos will force Flash on a desktop OS, to ensure the potential ad is seen (due to Google not adding this to their HTML5 player yet). It's either going to be the popover ads, or the preroll kind. I'm assuming a cookie is being used to know when the last time was when you saw an ad, since preroll ads don't occur all the time, but tend to appear if you watch a few different videos in a short time span.

On mobile/non computer platforms where they can't force an ad due to the lack of Flash, they uploader can choose to just not show the video, but this is rare.

If I put on my Google conspiracy hat, I'd say that this is all due to the new focus Larry had brought to the company. An ex Google employee who was pretty far up the chain as one of their main testing engineers wrote about it here:

http://blogs.msdn.com/b/jw_on_tech/archive/2012/03/13/why-i-left-google.aspx

One choice quote from the article:
Originally Posted By: James Whittaker
The old Google made a fortune on ads because they had good content. It was like TV used to be: make the best show and you get the most ad revenue from commercials. The new Google seems more focused on the commercials themselves.