ClickToFlash is a WebKit plugin. WebPlugIn plug-ins are new, based off a new Objective-C API.
Chrome/Mac currently supports the older Netscape CFPlugIn-based API, but not WebPlugIns. So it’s not just a matter of flipping an Info.plist flag or recompiling ClickToFlash to support Chrome — it may need a re-write.
I haven’t really looked yet so see what work it would take — we may be able to create a plug-in API bridge of sorts that allows ClickToFlash to target both browsers simultaneously (though you’d probably need to separate binaries).
I talked to Chrome’s plugin API engineer at WWDC09, and she’s down with ClickToFlash and wants to help us light it up. Happiness.
Interestingly, I think this would also give us Firefox support.
Update: Now it doesn’t look like we’d get Firefox support for free. Don’t really care, since I hear good things about Flashblock.