NOTICE:

1. This is completely based on my own thinking and understanding, and it's subject of being right or wrong, so think before you give in or out about my thoughts.
2. I might not be able to correctly translate the verses, but I'll try to make them as correct as possible, you might refer to it later in a correctly translated book.

It's been centuries that people have been using multiple ways to hide their intentions and to legalize their action for their own benefits, One of the many ways they used was religions, which was really disturbing for many people through lives.

From my position as a Muslim, I've been disturbed by the many stereotypes people have had about my religion, starting with being a religion of “Hate”, A religion of “Slavery”, and so many other types that you can't just count. I must admit that this was caused by us, I can't say everyone was, but there was a lot of people prototyping the religion in a way that there was no way of believing that this religion is not what it seems to be..

Of course I won't be able to list every single controversial thought about Islam, but at least I could show you a little of what I believe this religion to be.

Otherwise before we get into this, at first I'd like to declare some of the known controversial thoughts in Islam that had a great mis-understanding between different cultures.

1- “Kaffir <كافر>” Means “Disbeliever” Which is someone whom “refuses to believe in; reject in some belief”, Which now days may be subject to a lot of terms.
2. “Jihad <الجهاد>” Literally means “struggle”, Is an act of struggling against something for a belief or a reason. In Islamic means, it's used to describe an act to defend dangers and evil, Which was widely used to legalize many actions that are even forbidden in Islam.

1.“Religion Of Hatred”
It's been a wide known thought about Islam, That it's a religion of hate towards anyone who has a different religion or a different thought, Which is completely far from the truth.

In Quran it has been declared that no-body should be forced to join Islam, and it's forbidden to force anyone to Join Islam, It also has been stated that our prophet “Mohammed <Peace Upon Him>” only came to warn & guide people of the wrong action and/or beliefs they might have had.

Quran Chapter “88 Verse 21-22” “Remind them, as you're their reminder(21); you're not their dominant (22).”
2.”Religion Of War & Terror”
Islam always encouraged peace, War was only needed to defeat invasion and evil. Which also has very hard and strict laws in such an act. One of the simplest ways to understand such a principle is to translate the name itself, “Islam <ألاسلام>” is an Arabic word which in a religious context means
“voluntary submission to God”, Which also relates to the word “Salam <سلام>” Which means “Peace”. In which principle is shared between all Religions, Since there is no Religion that encourages War or Terror.
The following verse, clearly states that you shouldn't excess someones limits, only defend yourself against who fights you.

Quran Chapter “2 Verse 190” “Fight in the cause of Allah(God) those who fight you, but do not excess their limits, as Allah(God) does not love transgressors”

As for the following verses they should you what to do once you're offered peace. And strongly forbids discrimination.

Quran Chapter “2 Verse 192” “If they (your enemies) refrain, then Allah(God) is Forgiver, Most Merciful.(192)”
Quran Chapter “4 Verse 94” “O you who believe! When you go forth (to fight) in the cause of Allah(God), be careful not to discriminate, and say don't say to one who offered you peace: "You are not a believer," seeking the benefits of this life (so that you may despoil him). With Allah(God) are plenteous spoils. Even though he is as you were before; but Allah(God) had since then been gracious to you. Therefore take care not to discriminate. Allah(God) is ever Informed of what ye do. (94)”

As in the following verses, it clearly states that no body should kill without a proper reason. Taking in account time these verses came too.

Quran Chapter “5 Verse 32” “..we decreed for the Children of Israel that anyone who murders any person who had not committed murder or horrendous crimes, it shall be as if he murdered all the people. And anyone who spares a life, it shall be as if he spared the lives of all the people...”
Quran Chapter “17 Verse 33” “You shall not kill any person - for GOD has made life sacred - except in the course of justice..”

As for another source of laws is “Hadith”.
A ḥadīth (Arabic: حديث‎, pron.: /ˈhædɪθ/[1] or /hɑːˈdiːθ/[2]) (plural: hadith, hadiths, or aḥādīth) is a saying or an act or tacit approval or disapproval ascribed either validly or invalidly to the Islamic prophet Muhammad.[3] [ Source: http://en.wikipedia.org/wiki/Hadith ]

Book 021, Hadith Number 010.
Section : Prohibition against Killing Women and Children in Military Expeditions.

Yahya related to me from Malik from Yahya ibn Said that Abu Bakr as-Siddiq was sending armies to ash-Sham. He went for a walk with Yazid ibn Abi Sufyan who was the commander of one of the battalions. It is claimed that Yazid said to Abu Bakr, "Will you ride or shall I get down?" Abu Bakrsaid, "I will not ride and you will not get down. I intend these steps of mine to be in the way of Allah."
Then Abu Bakr advised Yazid, "You will find a people who claim to have totally given themselves to Allah. Leave them to what they claim to have given themselves. You will find a people who have shaved the middle of their heads, strike what they have shaved with the sword.
"I advise you ten things| Do not kill women or children or an aged, infirm person. Do not cut down fruit-bearing trees. Do not destroy an inhabited place. Do not slaughter sheep or camels except for food. Do not burn bees and do not scatter them. Do not steal from the booty, and do not be cowardly." [Source: http://www.hadithcollection.com/maliksmuwatta/192-Maliks%20Muwatta%20Book%2021.%20Jihad/19717-maliks-muwatta-book-021-hadith-number-010.html ]
This is it for now, later I'll be getting into other controversial topics that many people might've declared or understood differently.