it's a misintepretation of the Qur'an. The Muslims of the time knew the context of what Allah was saying when he referring to "kuffars" "unbelievers", etc. it was the Meccans who were attacking the Ummah (Muslim community). They had been patient and kind to them for about 13 years, waiting for them to stop, but they didn't so Allah gave them permission. Now, taken out of context, you can use these verses to justify violence against innocent civilians (And by out of context, I also mean these are the only verses you've ever read).
A lot of the wife-beating stuff is from the hadiths however. Hadiths gave mysoginistic Arab men the chance to revert a lot of the empowerment that Muhammad gave to the women.
there is however, a lot of stuff that terrorists fail to take into consideration. it is not simply an interpretational problem. For one thing, 9/11 killed about 300 Muslims. Now, it's a tremendous sin to kill another Muslim and to kill innocent people. Osama justified this by saying that the Muslims in America were infidels, which doesn't make any Islamic sense either, since you're not supposed to judge which self-declared Muslim is actually a Muslim and who isn't (Which is why I don't like Wahabbis, since they like to judge all Sufis and Shias as infidels).
Basically, the Qur'an says, for every innocent life you kill it is like killing all of humanity. When these violent verses were said, it was meant as a conventional warfare tactic, one army against another army. The killing of unarmed men, women, children, the elderly and monks is strictly prohibited. Since we can be definitely say the first four were in the WTC at the time, we can safely assume that Osama likes to twist the Qur'an to suit his own violent agenda.
Suicide bombers fall under this category too. How many people were actually attacking a suicide bomber when he went off?