These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The New 52 version of Nate makes it very clear that he won't work strictly for the government.
Bear in mind also that in the Bates and Weisman series, he was written as a former special operations officer, and was portrayed realistically as such. For those who don't know, it has often been said that if they weren't the most badass soldiers in the world, they would be hippies. Indeed, Cap more or less did become a hippy once he left the service during the Bates-Weisman run. The more hawkish government stooge portrayal came quite a bit later from writers who were obviously unfamiliar with the character or just didn't care.
Author's Saving Throw: In his Armageddon miniseries his government stooge persona under President Lex Luthor was later attributed to the fact that he was still depressed by his failed marriage to Plastique/Bette Sans Souci, so he went back to government work as a way to deal with the pain.
Complete Monster: Major Force is an Evil Counterpart of Captain Atom. The guy is responsible for one of the most infamous Stuffed into the Fridge incidents in comics (the Trope Namer, in fact). He murdered Kyle Rayner's girlfriend and stuffed her body in a refrigerator for Kyle to find. His idea of a joke? Pretending to do the same thing with Kyle's mother by putting what looked like her severed head in an oven. He's the worst possible person to choose for a military experiment that turns humans into powerful immortal Energy Beings. He is so crazy, he RIPS OFF Major Liberty's (his ally and fellow government cape) arm and beats him to death with it because, to quote: "We don't need two majors on this team!"
Narm: The third costume worn by the original Charlton Comics Captain Atom, a strange red/blue combo that replaced his yellow Mighty Mouse-esque costume. Even by Silver Age standards the third suit was just plain goofy looking.