Does Islam Forbid Protection to Non-Muslim Dwellings?
First, it is necessary to appreciate the status Jews enjoyed under Prophet Muhammad’s rule.
Islam does not consider Jews as “infidels.” They are referred to as the “People of the Book,” and have been afforded a position of equality . When Prophet Muhammad arrived in Medina, he promulgated the Charter of Medina. This mutually developed charter served as the constitution to govern Medina and forge an alliance between Jews and Muslims . Among its numerous progressive articles, Articles 16-19 explain Prophet Muhammad’s stance regarding Jews and their rights in Medina:
16. Those Jews who follow the Believers will be helped and will be treated with equality. (Social, legal and economic equality is promised to all loyal citizens of the State).
17. No Jew will be wronged for being a Jew.
18. The enemies of the Jews who follow us will not be helped.
19. The peace of the Believers (of the State of Medina) cannot be divided. (It is either peace or war for all. It cannot be that a part of the population is at war with the outsiders and a part is at peace). 
Thus, not only did Prophet Muhammad establish religious freedom for Jews, but he also ensured that Muslims were forbidden from supporting any enemy of the Jews. The Charter of Medina further added in Articles 21, 30, and 31, respectively:
21. Conditions of peace and war and the accompanying ease or hardships must be fair and equitable to all citizens alike.
30. The Jews of Bani Awf will be treated as one community with the Believers. The Jews have their religion. This will also apply to their freedmen. The exception will be those who act unjustly and sinfully. By so doing they wrong themselves and their families.
31. The same applies to Jews of Bani An-Najjar, Bani Al-Hárith, Bani Saeeda, Bani Jushám, Bani Al-Aws, Thaalba, and the Jaffna, (a clan of the Bani Thaalba) and the Bani Ash-Shutayba. 
These articles are clear—Jews are to be treated as one community, will enjoy religious freedom, except those who act against the tenets of justice. But the Charter elaborates further rights and responsibilities in Articles 38-42:
38. If anyone attacks anyone who is a party to this Pact the other must come to his help.
39. They (parties to this Pact) must seek mutual advice and consultation.
40. Loyalty gives protection against treachery. Those who avoid mutual consultation do so because of lack of sincerity and loyalty.
41. A man will not be made liable for misdeeds of his ally.
42. Anyone (any individual or party) who is wronged must be helped. 
Clearly, Prophet Muhammad established a unified sovereign nation based on religious freedom and mutual respect and trust. As Medina’s ruler, he ensured the Charter included Article 39—a requirement to seek mutual advice and consultation from the Jews—lest any party accuse the other of unjust or unilateral actions. Finally, Articles 44 and 49 hold both the Muslims and the Jews accountable for not fulfilling their obligation of loyalty to one another.
44. Yathrib will be Sanctuary for the people of this Pact.
49. The parties to this Pact are bound to help each other in the event of an attack on Yathrib.
Thus, the Muslims and Jews mutually agreed to protect one another from attack and to operate as citizens of one sovereign state. Rebellion against this democratic pact was treason. Even today, virtually every sovereign nation, including the United States and most of Europe, prescribes capital punishment for treason.
Critics claim that Prophet Muhammad had Abu Ráfi, Chief of the Banu Nadir tribe killed because, “infidels have no rights in Islam and their dwellings are not protected.”  They cite Ibn Ishaq to validate this claim. Ibn Ishaq explains why Prophet Muhammad ordered capital punishment for Abu Ráfi, Chief of the Banu Nadir tribe:
When the fight at the trench and the affair of the B. Qurayzah were over, the matter of Sallam b. Abu’l-Huqayq known as Abu Ráfi came up in connexion with those who had collected the mixed tribes together against the apostle. 
As historians have established, two Jewish tribes in Medina, the Banu Nadir and the Banu Quraizah, revolted against Prophet Muhammad and the Muslims while Medina was being attacked.  These tribes were eventually exiled for treason. And, as Ibn Ishaq reports, Abu Ráfi was the tribe leader who ordered the treasonous act in direct violation to the Charter of Medina Article 19, Article 30, Article 31, Article 38, Article 42, Article 44, and Article 49. These Articles bound Muslims and Jews to help one another should Medina be attacked. Likewise, Bukhari records, “Abu Ráfi used to hurt Allah’s Apostle and help his enemies against him.” 
Therefore, Abu Ráfi was not executed because, he was an Infidel whose home was not protected. Abu Ráfi was executed because he encouraged treason and actually rebelled against the state of Medina, despite signing and ratifying the Charter of Medina. Innocent people lost their lives because of Abu Ráfi’s treason. What government today would tolerate any citizen of the government who willingly helps the enemy harm the state?
Also, Ibn Ishaq reports the following about Abu Ráfi’s punishment: “As they left [to kill Abu Ráfi for his treason] the [Prophet Muhammad] appointed ‘Abdullah bin ‘Atik as their leader, and he forbade them to kill women or children.”  True to orders, the men did not harm Abu Ráfi’s wife, even though she nearly foiled their attempt. Wilders is wholly incorrect to paint Abu Ráfi’s punishment as a pre-emptive attack. Abu Ráfi’s punishment was the just, previously signed to and agreed upon, consequence of treason against a sovereign state.
 Qur’an 3:65, for example, says while referring to Jews and Christians, “Say, ‘O People of the Book! come to a word equal between us and you — that we worship none but Allah, and that we associate no partner with Him, and that some of us take not others for Lords beside Allah.’ But if they turn away, then say, ‘Bear witness that we have submitted to God.’”
 Charter of Medina art. 1 states, “This is a document from Muhammad the Prophet (may peace and blessings of Allah be upon him), governing relations between the Believers i.e. Muslims of Quraysh and Yathrib and those who followed them and worked hard with them. They form one nation – Ummah,” available at http://www.constitution.org/cons/medina/macharter.htm via The Constitution Society, a non-profit organization established in 1994 dedicated to research and publication of constitutional republican government.
 Geert Wilders, Marked for Death: Islam’s War Against the West and Me, 23 (2012).
 Alfred Guillaume, Life of Mohammed: A Translation of Ishaq’s Sirat Rasul Allah, 482 (Oxford University Press, 1955).
 PBS, Muhammad: Legacy of a Prophet, available at http://www.pbs.org/muhammad/ma_jews.shtml (Last Visited August 12, 2012).
 Bukhari Vol. 5, Book 59, #371.
 Alfred Guillaume, Life of Mohammed: A Translation of Ishaq’s Sirat Rasul Allah 482 (Oxford University Press, 1955).