(Reposted from the Iron Man Message Board, in response to the usual bitching about Matt Fraction's run)
Science isn't bad, but weapons are. And the problems with Tony's character are thus;
A.) He started out making weapons. He wasn't a civilian scientist who helped the war effort against a common enemy, he was an arms manufacturer from the start.
B.) He made billions off of the weapons he designed, and was very conspicuous about the way he used that money. Wearing suits that cost more money than an Afghani family makes in a year, paid for off of land mines that maim and kill those families, isn't in good taste.
C.) Tony's wars have never been the wars for which America is proud. In the past, in-comics jingoism aside, he was associated with Vietnam. In recent years, he's been associated with Afghanistan and the War on Terror. Regardless of your personal position on either of those wars, neither has been a particularly good mark on America's reputation.
D.) Up until that one fateful trip, Tony was never a soldier. He didn't see combat himself, and left his devices in the hands of the actual fighting men and women risking their lives. Even as Iron Man, he goes into combat insulated in a metal prosthesis that does all the fighting for him. At least in the past he entered combat with a heart injury and was truly putting himself at risk each time, but once his ticker was fixed, he was hardly facing opponents stronger than himself most of the time.
E.) Tony didn't even make his money himself. He made Stark Industries more successful than during his father's tenure, but he already had millions upon millions with which to start. The hardships he knew were from his father's disdain, but to most people, that just comes across as "poor little rich boy" syndrome.
F.) Even once he became Iron Man and stopped making weapons for others, he still made himself a symbol of imperialism. A billionaire playboy, putting on an ostentatious gold-and-red war suit, entering combat with a weapon that may avoid accidentally launching missiles at wedding parties, but has no problem shooting brown people with guns. That line is paraphrased from a particularly insightful (if harsh) assessment of the movies...
Basically, the problem isn't that Tony's a nerd and not a jock, or even that he's about science and not procreation. Even if he wasn't deliberately evil before he became Iron Man, even afterwards he represents a global system of profound inequality and constant struggle. The ending to issue 500 was the worst-case scenario of Tony's fears-- that he'd never do enough good to make up for his sins. The ending, however, had his daughter live in a society starting from zero, so at least Tony's sacrifice earned humanity a second chance, with a new generation that can at least make their own mistakes instead of having to struggle with their parents and grandparents' sins.
With Iron Man, you can either try to ignore these concerns and play the character as a straight superhero genre story, or you can deal with them. If you choose the latter, as Matt Fraction has done, you're dealing with an extremely tragic narrative.