The "Not all are the same"-argument is one from the worst ones. Supposedly it is intended to protect the majority of the peaceful Muslims. In fact, however, the extremist minority is not or only insufficiently affected. If a rapist is drifting around, it is not enough to justify the fact that the majority are not rapists. In addition, these 99% of the peaceful Muslims are in anyway nothing else than a lie. Studies and statements from Muslims themselves are proving that although not a majority, but enough of them have an extremist worldview and approve even violence in the name of religion.
If it were only 1%, then
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Erdogan would not have nearly 50% of the votes and 18% would not vote in Turkey for the right-wing extremists MHP whose members have to take an oath to the Koran
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the mullahs in Iran could never have seized power
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the Taliban would not have brought much of Afghanistan into their control
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Mursi in Egypt would have won not the elections, although he represents the Muslim Brotherhood, hence violence and terror in the name of Islam
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then the Saudi royal family and the Wahhabi clergy would have been long ago overthrown and the country would have modernized itself already
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there would not be so many Muslims celebrating every terrorist attack
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there would be no such problems with the Muslims and the Islam
And even if it were only 1%, the terror attacks from 9/11, Charlie Hebdo, the assassinations in London, Paris, Madrid and the countless other small and big attacks of the extremists on non-Muslims or moderate Muslims are showing clearly that already few are sufficient to cause great disaster. Since it is not only 1% but much more, you can imagine by yourself what will happen when they grab even more power.