The jury is very much still out on that one.
Plenty of web sites are still Flash-based at least in part, and big companies are still throwing serious money behind them, and this is several generations of iDevice-without-Flash later.
Meanwhile, subjectively it seems like the number of complaints from people using iDevices when they can't use a site for this reason has been growing a little, at least on the forums I follow.
The difficulty for Flash, though, isn't just that it has the issues that come with being a plug-in. It also has the issues that come with its development environment and underlying programming language, which have many of the same strengths and weaknesses as other tools these days, so there is nothing you need Flash to do any more. I doubt Apple can kill Flash alone, but a combination of HTML5, JavaScript, better distribution systems for native executables, new JVM languages running as applets, and any number of other technologies might well do it in the longer term.
I imagine Adobe are well aware of this, as they have been promoting a lot of alternative (and potentially much better) approaches to their traditionally Flash-owned territory lately.
Right now flash penetration continues to be massive.