Can't see FAT32 and NTFS external partitions on OS X El Capitan when SIP is enabled
The reason that FUSE will not run with SIP enabled, is that (amongst other things) SIP blocks changes to the /sbin filesystem location by default and this is where the "mount_XXXX" executable lives.

Instead of turning SIP off completely you can disable just the part that protects the filesystem support by running the following command in a recovery console.


  csrutil enable --without fs


This is the recommended way to get the NTFS module working in FUSE by the people who maintain OSXFUSE.

Note that the command will give you the following warning but it will work for now.


  csrutil: requesting an unsupported configuration. This is likely to break in the future and leave your machine in an unknown state.