Impression given by the news - as well as Mozilla pushing Firefox the same direction - would be that users have to - but also can - explicitly whitelist NPAPI plugins (such as CDF plugin) at least for some time. Complete removal of NPAPI is going to be a bigger showstopper in this regard, and Chrome developers are looking forward to perform this removal of functionality. The enabling reason for this is that web standards have matured, and practically all functionality that has traditionally required Flash or some other custom runtime is now natively implemented using these standards in most or all major browsers.
In many talks over roughly last year or so, Wolfram Research folks have been using wordings that would imply push towards plugin-less solutions (talking of "on any device" usually indicates this). Technologically modern Web stacks are sufficiently capable of running all the front-end functionality included in the CDF plugin, but the question where kernel functionality might reside is a different question altogether. For some content the answer is clearly "in the cloud" - but I don't believe this would be service free for all.
While CDF plugin provides the power of Mathematica kernel on the user device, it also limits the audience as most mobile devices are excluded from the picture, and barrier of adoption for NPAPI plugin is even at best a bit of a nuisance. I bet there shall be news on this front later this year.