How To Hide 'Frequently Visited Sites' In Safari on OS X El Capitan

Safari 9.0 has added a way to hide those frequently visited sites on the Favorites page.

The favorites page in Safari displays your favorite bookmarks with big icons. After surfing the web for a while, frequent sites that you have visited will also be listed.

To hide frequently visited sites in Safari 9.0, right click on the Favorites page, then unselect "Show Frequently Visited Sites".