Here are some steps to troubleshoot when the Web Application Availability Monitor is not instantiated in the SCOM console (the green circle is not filled ).
1. Check the URL designed to be monitored from the server configured in the monitor.
2. Create a new monitor for a web url that works, for example www.bing.com .. if this does not work either->
3. check the run as credentials. These are stored under the run as profile
Microsoft.SystemCenter.WebApplicationSolutions.RunAsProfile.Configuration and is part of the "Microsoft System Center Web Application Solutions Library" Management Pack
If there some issues with the credentials, you will find the workflow failing in the Operations Manager Event Log. You can search for "WebApplication" since there are a couple of different workflows which need to be successful so that the websites are monitored.
If you monitor URLs from the SCOM MS directly it would be a good idea to delete the run as account from the Microsoft.SystemCenter.WebApplicationSolutions.RunAsProfile.Configuration run as profile, since when no other account is configured, then the default action account will be used.