Is there a way to disable click-to-play for the PDF plugin only — that is, just let the PDF plugin always run, but still use click-to-play for all other plugins?
This should be possible with the contentSettings API in Chrome 15, in that you could enable the PDF plugin for all urls, but the option to change per plugin is not yet built-in to the browser (see crbug.com/106917).
Instead, you can install the Per-plugin content settings extension, go to the extension's options page, select the PDF viewer, and enter
<all_urls> as the hostname pattern, and select "Allow".
This will make the PDF plugin run on all sites while leaving other plugins as the default (e.g. click-to-play), hopefully this will make password-protected PDFs work as well.
Update: Chrome 17+ now includes an "Allow" checkbox next to each plugin in the chrome://plugins page to do this, but it is not as flexible as the extension linked above.
You can enable Click to Play for plugins and then go to about:plugins and select the "Always allowed" checkbox for the plugin(s) that should always load such as Chrome PDF Viewer. This setting overrides click to play and the automatic plugin blocking.
No, this is not possible. You can, however, add a particular website to exceptions list so that you can always allow plugins from that site.
The exceptions list is for websites only, not plugins. If you're accessing PDF files from a particular site, you can make use of this option.
The Exceptions list can be found at Chrome Menu → Settings → Show Advanced Settings → Content Settings → Plug-ins → Manage Exceptions (or from