Angel Densetsu, Toradora! Recommendations
In these two serialisations, we follow male protagonists who have a scary appearance, but are kind-hearted.
Both of the main characters have frightening appearances that makes other people think they're thugs even though they're actually nice. Both of these are school life comedies, although Toradora is more romance oriented than Angel Densetsu. 
Both are comedy romance manga with characters in highschool, and in both manga a member of the main pair gets into trouble for looking/being scary, and the other one helps them integrate themselves more.