I have opened After Effects CC multiple times, created and saved .c4d files from Cinema 4D Lite and dragged .c4d files onto both applications. I have also restarted the computer many times. The system is running on a new installation on Mac OS on a drive formatted just 2 weeks ago so there should be no issues from strange system changes.
The .c4d files still appear with a Terminal icon and association on Mac OS X. Even when I use "Open With". This is annoying because it is hard to visually find these files without the proper icon on them. They even have the Terminal icon when imported into After Effects.
How can I change the icon system-wide to be correct?
Unless you have a full version of C4D you will have to open C4D lite from inside AE. It's part of the licensing agreement and there is no way around it.
The Mac user forums have tutorials on creating a custom icon for file types. I'd look there. You can't associate C4D files with C4D lite because of the licensing.
Generally one would right-click on a file, use Get Info and then set a default program, but as Rick said, if you only have C4D Lite that doesn't do anything. It won't run outside AE.