This is a question that is dear to my heart because during my life growing up in the USA for the past 35 years I have been witness to both improper conduct by Muslim Organizations against Individual Muslims as well as against Muslim Employees. The reason why this issue is tricky has to do with the way the majority of Muslim Organizations run in the United States. The money they all get in donations tends to come from the public, which usually includes other Muslim Organizations. This heavy reliance on the public, due to restrictions on foreign money coming in, has damaged the sincerity of Muslim Organizations that should be watching out for Muslim's dignity and rights.
For example, if you go to a Mosque and the leadership kicks you out due to your race, sect, ideology, or gender...who do you turn to?
Or for example, if you work for a Muslim company and they wrong you, who do you turn to? At first it appears simple and easy, you think well maybe I can report this to the EEOC or ACLU. However, if you look deeper it is not that easy, because as soon as any regular organization that is not Muslim decides to do something about the issue at hand, they may fear being persecuted for being "Islamophobic" or having some sort of anti-Muslim agenda. So, as an American Muslim you are caught between a rock and a hard place. You can neither ask help from regular organizations and you can't ask for help from other Muslim Organizations.
This is why I think it is necessary for Muslims to form new organizations such as "The Muslim Internal Affairs Department of the United States of America" or MIADUSA...or "Muslim Internal Affairs of America" or MIAA. Infact, I am currently talking to colleagues across the nation regarding the formation of such an organization. If you are an interested party, please email me at http://www.freecontactus.com/contactus.php?id=4288
We have been so busy since 911 trying to stand up for the rights of Muslims in America that we have forgotten to look inside ourselves, our communities, and our organizations. No organization in the United States has a monopoly on Muslims or represents all Muslims in the United States. There are too many Muslim groups for that to actually take place. You would need to have a body of organizations that would approve of the Amman Message that was signed in Jordan or the famous "Shia Fatwa" that was given out by the Al-Azhar University in Cairo, Egypt. Al-Azhar is considered the top Sunni Muslim University in the world and has been around since the Fatimid Dynasty in Egypt. This defensive focus in order to protect the Muslim community against external hate, biggotry, and racism has in a way blinded our communities from the problems within. Just look at the young guys that were marching off to join the Al-Shabbab / Al-Qaeda group in Somalia that were caught in New Jersey. They are an example of how we as a community have lost focus and attention of our youth and internal growth and progress. There are a handful of American Muslim Organizations that are doing their best to educate people and work on internal problems, however they are usually not funded as well as other organizations that may receive money from overseas.
I remember talking to a young man in the community a while back regarding his involvement with local Muslim Organizations in Columbus, Ohio and he replied to me with this smirk that any help or money he or others would give would not do anything for him or the downtrodden Muslims in America. This sense of apathy, dissapointment, and hopelessness is sad. It is really sad because we have a lot of talented people in the American Muslim community that can contribute to a better world. However, they are not given the opportunities necessary to create change. I pray that this situation changes so that American Muslims can have a voice when they are wronged not only by Non-Muslims who may have hate towards them, but also from other Muslims who mistreat them and stifle progress. So many good leaders in the American Muslim community have been stifled due to lack of understanding and vision. Until we appreciate our leaders and community members who have true vision for our communities, the organizations are nothing but unmanned vehicles without progressive guidance. God knows best.