I think I and a few others who have a large amount of experience on both sides of the fence have bridged the gap pretty well regards the OPs question. In fact, I'm nearly even between the two. There are similarities, there are differences; and a good question that was answered was when the OP asked "how come I can't use my civil ratings and become a mil pilot instantly?", which was a valid question that was answered.
There will always be bad apples from any side of an equation that will taint the rest of the batch. Don't let those broadbrush your view of the batch towards the negative, whichever side is being discussed.
And for the record, while I think I can handle a UH-1 pretty darn well, I'm in no way qualified or experienced to be working the pattern on a moving FFG in day VFR with calm sea state, much less anything worse; unless its a major emergency.
I think it has been said before but my thoughts are this and maybe inline somewhat with the OP. The fact is anybody can fly GA, within reason of course. Not anyone can fly military, there is a process to go through to get into the cockpit (college, API, flight school, etc). Like Hacker said, some folks don't want to go through the process or maybe, put up with the BS that comes along with being in the military but they are certainly more than capable.
Military pilots aren't naturally better pilots than anyone else IMO. The training and experience is second to none of course; it's extensive, thorough, competitive and of course in flight school, you're always in worry of not making it through. I often have people tell me how hard it must be to fly off carriers. I guess hard is a relative term as we are trained to do it and IMO, it isn't that hard with the training. In the year I was at VT-4, we had around 36 advanced students go through and 3 did not make it...all were DQ's at the boat. That's a good ratio actually and it comes down to wanting it and the training. The FRS and fleet come next, in all my years in E-2's and C-2's, I only know of two folks who were FNABED for the boat. Might be highter in the jet community, I don't know. For me, flying around the boat just brings you to another level. Landing at night on the carrier was the single most difficult flying accomplishment for me. For a fighter guy or an attack pilot, it might be the air-to-ground or air-to-air portion that offers that ultimate challenge.
With these intense flying challenges (for lack of a better word), comes confidence overtime. Maybe even pride and folks might see that as cockiness or having a superior attitude. There certainly is some of that, you don't come away from those experiences (like night carrier landings) without some sense of pride, accomplishment and achievement. However, with that comes some humility. If you don't have it....such as when switching over to something like GA, it can be deadly. I certainly agree that being a good fighter pilot or ball flyer at the boat does not make one a good GA pilot. Knowing the airplane and the rules that govern the GA regime of flight is critical. To enter into without knowledge and preparation is a recipe for disaster.
My old AOIC prior to my 2006 deployent was a good man, from the little I time I knew him. He had maybe around 1000 military hours, mostly C-2A Greyhound but also flew the T-34C, T-44A and the T-45A Goshawk advanced jet trainer in training. He was a civilian rated pilot too, his family owing a RG Cessna, not exactly sure which one. To make a long story short, he took his brother and father fliyng up in the mountains to see some homes his brother was building. He ended up getting low, slow in an overweight and underpowered GA aircraft. A mountain eddy caught em, he stalled the aircraft, departed flight and all three were killed. From what I remember, he was a good ball flyer and competent military pilot. Nobody is immune from getting behind and aircraft, military or GA.