Raahim,
I agree that there are many people who don't know anything about Islam who criticize Muslims without trying to see the whole picture. And of course I agree that there are many Muslims fighting the very few terrorists there are in the world.
You bring up a comparison with physics. Okay, let's go with that. Physics is a tool we use. Good people can use physics for good purposes, and bad people can use physics for bad purposes. Are we good so far? But notice that physicists are free to experiment, find better answers, and discard old, no longer useful ideas.
Islam is also a tool that can be used for good or for evil. But there are a few problems:
First off, the most natural and obvious understanding of the Quran is that it promotes supremacy, misogyny, anti-semetism, homophobia, and intolerance in general. Over 1300 hundred years of Islamic history demonstrates that millions and millions of Muslims have consistently interpreted the Quran exactly as I have just described. So you can claim that those millions of Muslims got it wrong, but I don't care! As long as so many Muslims continue to get it wrong, it's a dangerous tool.
Second: By its own definition, Islam's ability to evolve is severely limited. For the most part, we're stuck with a vision of the world that came from people who knew almost nothing of the world. This isn't to slam 7th century Arabia, this was the state of the entire world 1300 years ago. I am happy to grant you that Islamic teachings were very useful in a primitive, tribal, hostile slice of desert. But the world is very different than that now, and we cannot afford to give such out-of-date, tribal messages any power. What we've seen for 1300 years is that far too often, Muslims use Islam for evil.
Just to save time, much of what I just said about Islam, is also true of Christianity.
I won't bother much with this because @DawudTalut answered this issue and I agree with it.
But "...far too often, Muslims use Islam for evil." - So does every other religion, don't you think so? You might not agree with any religion, but Christianity for example is much worse and violent in practice than Islam, I won't bother proving this because same old statements will be used with which I don't want to bother at the moment. If you can't apply Islamic views to modern day that just proves you're not very well educated in Islam.