I once thought of porting it over to run on Ubuntu, but I read over the source, realized that Notepad++ uses the Win32 API quite extensively and quickly abandoned my plans. Ultimately, I would have ended up writing/supporting a totally new editor...then dealing with legions of people who are angry that my first 0.1 didn't provide an exact 1:1 feature match of Notepad++.
You might still need to deal with gcc/msvc compatibility issues and the end product would only be slightly more native than running it via wine.