im sorry, but that article was crap. Im sure there are some soldiers that do not like gays serving. Im sure there are also soldiers that do not like blacks, or whites, or women, or ... serving, but getting a few anonymous comments amongst 6 figures of troops is not indicative of anything.
There may very well be a strong bias, but the article did nothing to confirm it. FTIW, I know a marine veteran that served in iraq who while not gay, is totally cool with gays. he almost lost his life fighting in some of the worst battles (fallujah, etc), so maybe I should anonymously quote just him and make the military out to be more enlightened than it is.