How do I get rid of "Network may be monitored" in KitKat?
I was looking into the same issue, and it was answered on XDA http://forum.xda-developers.com/showthread.php?t=2537794

In short - it is possible if your phone is rooted to move the certificate to the System section.

Very annoying that it is not possible to exclude certificates from this warning - it only produces noise when I know that the cert is OK to use.