There were some early font issues in El Capitan, and with font managers (third party and Font Book). But those have been cleaned up one way or the other.
"Due to security measures in OS X 10.11 (El Capitan), PostScript Fonts need to be located somewhere in your Users directory, such as /Users/[username]/Font Folder in order for them to work properly in some graphic applications…" That's the problem.
That was a problem and no longer is, as long as you're running at least 10.11.3. The bug was not PostScript itself since OpenType PostScript fonts worked fine. What you couldn't do is put Type 1 PostScript or older legacy Mac TrueType fonts in the root /Library/Fonts/ folder. They just wouldn't work from there and had to be in the Fonts folder of your user account. That has been fixed.
The remaining bug (haven't checked to see if it's been fixed in 10.11.6) is that fonts won't always release when disabled. The test is to open any fonts, type with them in any app and then disable the fonts. Any app should then tell you the fonts you were using are not available and change the fonts in the app to something that is. Which they would do - the first time. Re-enable those fonts and type again. Disable them again. The second time, nothing happened. The fonts would still show in the app and you could keep adding to your text as if they were still available. Only closing the document and reopening it would cause the app to finally tell you the fonts weren't active. The folks at Extensis checked and found that yes, the fonts were really disabled, but it appeared El Capitan was still working off of font cache data that wasn't being updated to match what was open. This is/was a fault you could duplicate with any font manager, including Font Book.
Anyway, I use Suitcase Fusion 7, and it works fine. I've also tested the current version of FontExplorer X Pro. It also works as expected.
To start with something simple, shut down all apps, including FEX and Font Book, if the latter is still on your system. In the Preferences folder of your user account, put these two files in the trash and restart:
com.apple.FontBook.plist
com.apple.FontRegistry.user.plist
One keeps track of Font Book's basic preferences and which fonts are active. The other, which fonts have been disabled in its interface, so you may not find both.