Pen cursor in Xournal
If anyone else is still having trouble with this, you can change the cursor type in settings now.
For Xournal++:
Edit > Preferences > View > Cursor
For the original Xournal:
Options > Pencil Cursor
I found the following work around from 2010:
change the following lines in ~/.xournal/config
highlighter_opacity=.99
startup_tool=highlighter
highlighter_color=black
highlighter_thicknesses=0.85;1.41;2.26
This changes the default tool to highlighter, makes the color black, opaque and gives it the same thicknesses as the pen tool.
Here's where this was suggested:
http://sourceforge.net/projects/xournal/forums/forum/554376/topic/3867709?message=8665099
Maybe I should submit a feature request.