I think US issues with Muslim-dominated nations are overblown. We must also consider the branch of Islam and its relative nature of liberalism or conservativism. The same thing holds true for Christianity. Some branches of Christianity would like to outlaw vaccines, stem-cell research, ect. There is nothing in the Koran about forcing people to convert - that is a small strain of Islam called Wahabism which developed in what is probably the US's biggest Arab ally: Saudi Arabia. They are a minority but their actions make a lot of noise akin to radical Christians who perform terroristic acts such as abortion clinic bombings and doctor assassinations or gay beatings.
Further, many of the issues the US faces in the Middle East (ignoring the fact that we have fairly amiable relations with many of the nations and the Arab League [I understand Islam and Arab are not interchangeable but they are undoubtedly correlated in Western minds]) are the result of the US historical role in propping up puppet governments in former Ottoman territories. We have supported dictators in favor of stability and now must explain ourselves to people who feel we aided their oppression. The biggest positive is that many young Arabs and Islamic Arabs are in favor of democracy and its associated freedom of religion. Egyptians feared the choice they were left with when more moderate/liberal candidates barely lost out in their election (44% of vote split among a couple candidates: 22% each) resulted in a run-off between an Islamic Party and the Military Party of the past.