Prophet Muhammad wanted to eradicate polythiesm and all practices associated with it, such as doing tawaaf around the kaaba naked.
Surah Tawbah was revealed, which included a message that the idolaters should not be allowed near the kaaba after this year. The Prophet first sent Abu Bakr to share this news with the Meccans, but then God instructed him to send Ali instead. The message was that the polythiests would be banished from Mecca after four months, except for those who had treaties that lasted longer. Those who asked for safety would be granted it after being taught about Islam. But shia and sunni views of this even are discussed.
Surah Tawbah is the only surah without a bismillah, and it contains many references to the idolaters, and how to treat them. It defined the rules of engagement against those who would fight agains the Muslims and that they should be granted asylum if they seek it.
The banishment of kuffar was similar to how governments today determine what speech is harmful and what the accepetable overton window for a soecity is. Even liberal governments have ideologies they don't tolerate.
Lecture notes available at http://www.why-quran.org/?p=746.
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