You have to realize that these issues aren't particular to Islam. I don't know why you single it out. Christianity is also peaceful, Christ was called "The Prince of Peace," but through the centuries there have been countless acts of violence perpetrated by Christians. The same is true of Jews, Hindus, Buddhists, and probably every other sect you can find.
You should also realize that like all those religions, there are different interpretations and groups within them that apply their religious ideologies in different ways. Most Muslims, Christians, Buddhists, Hindus, etc. do not assault homosexuals, abuse women, kill heretics, make war. But, those that do are bound to get a lot of attention because those actions are so far outside the norms of civil behavior.
To take the cliche comparison with Christianity: during the Inquisition, murder of heretics, Jews, and other non-believers was programmatic. Christians killed Jews, Muslims, and other Christians in the decades long assault on the Holy Land during the Crusades. There were unbelievable atrocities committed during the Reformation and the Counter Reformation. Although it's a more recent development, homosexuality is vehemently despised by some Christians, and in some countries it is a crime punishable by death. Uganda's homosexuality laws (which were drafted with the help of a few American Evangelicals) criminalize homosexuality as a capital crime. Wife beating was long permissible by Christianity, and even the way it could or should be done was prescribed. And so on. All the horrors that you ascribe to Islam can also be found in other religions and often for the same reasons.
Because religions rely on sacred and immutable texts and because language is always a little unclear and because people are always willing to be either more or less horrific, you will find that religious people believe and practice the same religion in different ways. Usually, most of the people following a given doctrine act basically according to the cultural norms while a few people take the same doctrine to some really extreme, dark ends. To say that Islam is a peaceful religion misses the point as much as saying that it is a violent religion. It contains both and cannot be one of the other by default. It is a religion and religions are made up of people and people are generally communitarian and peaceful, though they can be incredibly cruel.