Is it safe to disable System Integrity Protection? While using OS X El Capitan 10.11.x, is it safe to disable System Integrity Protection? There are all these additional apps that modify folders and the dock that I want to install but you have to disable rootless first.

Good idea or bad idea?
If you disable SIP you'll get the same level of protection as you had with OS X versions before El Capitan. Whether this is enough for your needs it something only you can decide.

OTOH it's not that much trouble to disable SIP briefly to chance a protected part of the system. If you want to be on the safe side, disconnect from any networks while you do this.