Is it legal if I applied for a job which I am more than qualified but the company sent me a letter stating that they would not hire me because I am not a member of their church?

That *may* not be legal: employers are prohibited from discriminating against an employee or prospective  employee--such as by refusing to hire him or  her--due to his or her religion. There are limited circumstances where an employee's religion or church-affiliation can be taken into account, such as--

* If the employer does business with that church, and has a policy against hiring anyone from any of its customers or business partners;

* If the employee's religion would directly prevent him/her from doing the job (e.g. an observant Jew could not be hired to work at a restaurant or catering hall if it's required to work Friday night and Saturday--that's when most of the business is done)

--but apart from cases like the above, an employer should not be considering a  prospective employee's religion when making a hiring decision. You may have a claim for illegal religous-based discrimination; you should discuss the matter with an employment law attorney or speak with your state's equal/civil rights agency.

Based upon what you have written, you were illegally discriminated in the work place based upon your religious affiliation under the laws of all states in this country.

I suggest that you consult with a labor law attorney and/or see a representative with your local Fair Employment and Housing as to what your legal recourse is.