A current survey of thousands of the most popular web sites finds that Adobe's Flash software is present on almost half, 47% as of March 29. That's down from 56% when the survey was initiated back in October 2010 but still a sizable proportion. Personally, I regularly hit sites with the iPad where I can't watch videos such as Boston.com.
There is one limitation in the data -- the survey of each web site indicated it was using the Internet Explorer 8 browser. It's quite possible that some sites serve a flash-based page to IE users but a non-flash page to an iPad or iPhone browser user.
But despite that limitation, seems like Apple has yet to kill off flash.