The following got FSL up and running on the 10.11 GM:

0. (may not be necessary) remove FSL

1. Install latest version of XQuartz

2. Download fslinstaller.py

3. Open fslinstaller.py in text editor and change line 1090 to for release in range(10,16): and comment out line 1092. Save.

4. Run python fslinstaller.py

Good luck!