OS X El Capitan keeps changing the auto hide Dock feature
As EDP pointed out Command+Option+D does this. The Spectacle app has shortcuts near this (+F for example) and I'll tap 'D' accidentally from time to time. Even if you're not tapping the shortcut inadvertently, Command+Option+D is a great way to switch the setting back when it's goes wrong.
If you want to prevent it, you can go to [Settings &gt; Keyboard &gt; Shortcuts], and disable the shortcut under Launchpad &gt; Turn Dock Hiding On/Off.
Cool trick: open [Settings &gt; Dock], and tap [Command+Option+D] a couple times.