The first thing that comes to mind is that the "real" Koran can only be read in Arabic, everything else is "the meaning of the Koran." I think this comes from "behold! I have given you an Arabic Koran, written in a clear Arabic tongue," or words to that effect. So pretty elitist there. I think this is also an example of why it's important to understand the interpretation of the Koran, not just what's written there in black and white.
I agree with you partially. I find it personally frustrating that I cannot (yet) read the "true" Quran, but part of me admires their devotion to keeping it as close to the original text as possible. A good example is Christianity. There are a bunch of translations out there that are so off the wall it's baffling. & any many cases, the English translations cannot capture the full meaning of the text (a good example is the part of Jesus telling Peter to "feed my sheep." The english translations utterly fail to convey the "emotion" of the story. But that's a different topic.
A couple of passages that IMO reflect intolerance of non-Muslims:
In regards to 2:191-193, the context is is in retaliation. The verse prior makes it clear that they are not to initiate the attack: "do not attack them first. God does not love the aggressors." It also goes on to say that "if they mend their ways, know that God is forgiving and merciful."
Likewise, 2:216 is set in the context of persecution the Muslims are currently facing. A couple verses later it shows that when it says "They will not cease to fight against you until they force you to renounce your faith." It's important to note the people Muhammad is fighting against here. Radicals like to pull verses like this out of context to support their cause, but they forget that Muslims really were being persecuted back then, & in a serious way. His criticism of the "capitalist" society is what got him in trouble. He despised the gaping space between upper and lower class, & advocating sharing wealth so the underprivileged were not left to rot. This old school socialism hit a cord with people, particularly the poor & women, who were among his first converts. Him preaching monotheism did not sit well with the big dogs, who made a huge profit off of the people who made a pilgrimage to Mecca to worship the pagan gods. In response, the Meccan big-wigs boycotted Muslims, which caused massive starvation & likely the death of Muhammad's first wife. Muhammad was then essentially recruited to help unite Yathrib, who had constant tribal feuds. So they moved up there, & Muhammad united the warring tribes, which was literally unheard of, since raiding caravans was one of the main ways they survived because of the terrible climate & agriculture. A bunch of people from Mecca migrated to Yathrib to follow Muhammad, who changed the name to Medinah.
Once all the tribes united, the still found out food was scarce, & there was no way to sustain life. So they ended up raiding a Meccan caravan, which led to war between Muhammad and Mecca, & the background for most of these violent verses.
Position of women within Islam:
I'll be honest, these verses bother me as much as the next modern-day American. But believe it or not, Muhammad actually furthered women's rights far beyond what it was prior to him. Like my Islamic Civ teacher said, "Muhammad took women from being objects to 2nd class citizens, which is a big improvement for the time" even if it doesn't appeal to us.
Muhammad was monogamous in Mecca. After his wife died & he married many women, which was completely expected, since it binded the tribes closer. I'm not going to try to justify his consumation of marriage to Aisha, who was pre-pubescent, because that's disgusting no matter how you cut it.
He also forbade the burying of infants- a common practice in his times. People did not want daughters b/c they were undervalued, so they'd bury them alive. He stopped that. He also allowed women to hold some property rights, centuries before the West ever did.
Another thing people despise is polygamy, but as sad as it sounds, it was a good thing for the women at that time. During these times, men were getting killed a lot in war, & men were the "protectors" of women. Without husbands, they were essentially "fair game" to be exploited, raped, etc. 4:3 explicitly states that you can have four wives, ONLY if your show no favoritism. Of course, that's impossible, but that's what it says. Other verses that give women a better deal than they had previously is 4:11, 4:32, & 4:35
Women still got the shaft, but they were far better off (initially) in Muslim society than they ever were prior to Muhammad.
I think another place to look for intolerance in the interpretation of Islam is to check out Bin Laden's "fatwas" and take a look at the passages that he uses to justify his actions.