Chances are you are seeing River Herring, Alewives or Blueback herring, which ARE protected.
Atlantic Herring are allowed but that is likely NOT what you are seeing in your waters.
The terms being used do not state where you find them but are nicknames for specific types of herring.
Go to this site and look at Alewife, Blueback, and plain old Herring
http://www.maine.gov/dmr/recreationa...ch/index.htm#f