Maybe people just click through because the current warning dialogs say little or nothing to them that they can understand or use to make any kind of rational choice. Maybe there are too many such dialogs (false positives, remember...). Both of these issues can be improved.
There are, of course, always going to be people you just can't reach or make understand what the software is saying. But that doesn't mean it's not worth trying to improve the current approach which uses obscure (even to me) references and terminology and provides minimal real, relevant information. It would be fairly easy to design improved dialogs for this sort of thing that provided a 2-3 sentence summary of the reason for the warning, e.g.:
"We've detected a program named 'myapp.exe' acting suspiciously on your computer, but it doesn't match any currently known virus. The unknown program appears to be trying to alter important files used by your operating system."
"The unknown program appears to be attempting to access the Internet in an unusual way", etc., e.g. on a non-standard part, or whatever, we're just dumbing it down here.
And then a prompt:
"If you're not sure whether this is legitimate behavior just choose to Quarantine the program and we'll suspend its activities. If you change your mind later you can always Restore it in your antivirus control panel, accessible from the system tray icon in the lower right of your screen."
And then you have one of those expandable dealies to get more info for advanced users, or an "Advanced Info" text button (don't make it look like something just anyone would want to click, i.e. not a shiny button). If a user clicks for advanced info they get a process name and path, and other info, maybe some buttons to open the process properties, or path, whatever.
That's just a simple idea off the top of my head. And I think it improves on almost every antivirus warning dialog I've ever seen. It would not be difficult or complicated to implement, every suspicious behavior heuristic maps pretty basically to a few simple categories like "unusual network activity", "trying to access or modify system files", etc. Just translate those into human readable dummy speak and put it in a friendly 2-3 sentence description.
Oh and yes, we need to make the messages mandatory to read, so use UAC prompts (why don't more antivirus apps do this when they detect problems!?).