Except you can find out that the actual nytimes.com site does use Flash (it was even obvious in the real life demo by Jobs). You can probably even find a copy of the HTML from the time that Apple cut the video, proving that they faked it. Screen images in videos like that are usually simulated, this isn't a huge surprise. They should have just used a site that didn't use Flash.
My argument still stands. This is only matters if you can argue that substantial numbers of people say "OMG it has Flash, _now_ definitely want one".
The question is one of intent. Did they want to intentionally want to make people believe the iPad has flash, or did they just want to have the NYT site look good/un-broken in the ad?
This complaint is making a mountain out of a molehill.