My biggest complaint is sIFR text replacement. Seriously, using Flash just to serve up a certain font for your H1 or H2 titles is complete and utter crap.
While I do think that this is bad user experience for those buying the MacBook Air, it should help foster an overall better user experience for the Internet.
With Flash not coming standard and Apple gaining so much market share, it will only be a matter of time before the percent of Flash enabled browsers falls enough that web developers need to start using more appropriate standards-based techniques.
Adobe claims that Flash reaches 99% of browsers: http://www.adobe.com/products/player_census/flashplayer/
Once that hits 95%, I think we'll start seeing a tipping point. About 68% of web browsers worldwide currently have partial HTML5 support (IE8+, Firefox 3.5+, Chrome 6.0+, Safari 5.0+, Opera 10+). That number is 72% in the US.
I give it two years until Flash and HTML5 are at parity with one another.