Returning a salute makes sense to me. He is the Commander in Chief, and even if he has no military background, that is a military title and he is being saluted by military personnel. To not return the salute seems to me like a snub.
Interesting, therefore, that President Eisenhower, a.k.a. General Eisenhower, did not return salutes. All I can figure is that he wanted to make some kind of distinction between his position as President, a non-military role even if he's Commander in Chief, and his former status as a General.
As for people stirring up shit about President Obama saluting whilst holding a cup of coffee, I agree that that's kinduv bad form, but to hold that up as some kind of example of how he disrespects our military is just stupid shit-stirring. President Bush returned a salute whilst holding a fucking dog, and it was a pretty lame salute overall.