I use ClickToPlugin with Safari as well and have no issues with it failing to block the Flash videos that are thrust at me. Given that it works for me I’m going to suggest that you check the plugin’s settings.
To do that choose Safari > Preferences and then select the Extensions tab. In the resulting window you’ll see a list of any extensions you’ve installed (or an app has installed for you). Select ClickToPlugin and be sure that it’s enabled. If it is, enable the Click this checkbox to access the settings option.
This causes Safari to create a new tab, which holds ClickToPlugin’s settings. Within these settings select the General tab and ensure that the Load plug-in if HTML5 conversion fails option is unchecked (see the image above). With this option disabled you shouldn’t see a video simply because Safari was unable to convert it from Flash to HTML5. As should happen, the video will play only when you click on it.