At American Airlines all military traveling to or from OEF/OIF get use of the Admirial's Club by flashing their orders. Once inside, I was told by a young trooper, you don't have to buy a thing, the frequent traveling business people take care of ya. Similarly, I have found most military do get special treatment when in uniform. Doesn't happen all the time, but frequently. With planes runnning full and airlines lossing money you won't get an upgrade if a guy from Microsoft wants to pay big $$ for the seat. On the other hand, the flight attendants will treat you well no matter where you sit.
About standing out. There is risk. If there is an actual terrorist incident, you will likely be the first targeted. It has happened before. Anyone remember what happened to the Navy diver in the 1980's? On the other hand, short of a complete, violent and instantaneous take over of the cabin, you may be helpful to the cabin staff. At my airline the fight attendants are trained to look for military types to help out as trusted agents in any emergency. You may be reseated to an exit row to help with doors. If an aviator, you may be asked to talk to the Captain on the interphone about what you see or hear (remember, pilots are not allowed out of the cockpit to inspect the cabin any more) or you may be asked to help secure a passenger. Military EOD personnel have been asked (not by my airline, but it has happened often enough that I am sure it is promoted)) to stop by the cockpit and identify themselves, in or out of uniform.
It is your choice. Weigh the risk. Is it more likely you can be off assistance in an emergency or minor security problem if readily IDed or is it more likely you will get a knife in the back of the neck while you play Halo on your laptop. Don't forget to factor in the occasional free drink

.