This is because video ads use an obnoxious ad API called VPAID [1] that is mostly used to track viewability of video ads (which in turn conditions the billing event for advertisers). This is most effectively done with Flash and so 90% of video ads use Flash if given the opportunity.
The NY Times' recent post about their transition from Flash to HTML5 video highlighted VPAID as one of their big challenges. It sounds like they had to pull the ad vendors, kicking and screaming, into the HTML5 world.
[1] http://www.iab.net/guidelines/508676/digitalvideo/vsuite/vpa...