When you write "AC protection" most people think of mains voltage (110-240V depending where you live). No, the Arduino has no protection against mains AC. It will simply emit a little cloud of magic blue smoke, possibly accompanied by a loud "pop".
You meant to ask if an AC signal (where the peak voltage is below 5.5V) on an input pin will damage it. No, no damage at all. It does not matter if it is a mixture of DC and AC. The problem is, can you get a usefull measurement?
On a digital pin, you will se the pin input change between HIGH and LOW at the frequency of the AC signal. If the signal is irregular it will switch just as irregularly, but be more often HIGH than LOW (due to how the digital input threshold is done.). On an analog pin you might expect the "DC average" over the time the port samples, but the way it does that, if the AC signal is in the tens-hundred-Khz range, you get essentialy a random value.
As others have said, if you want the DC component of your mixed signal put a capacitor in series and a resistor to ground, after your voltage divider, and you get some reasonable value for the DC part. Look up RC filters for usefull values. (The multimeter basically does this when you switch to AC measurement)
If the frequency of the AC is low enough you can measure the length of the AC periode on a digital port. If it is real slow, you can sample often and get the wave form.