Yes, federal law should protect people from any and all types of discrimination. When looking for a job and deciding if they should be hired the number one thing that should be considered is if they can do the job, not if you like them or agree with their lifestyle.
Legislation protecting people based on their sexual orientation is a noble and right thing to pass, but it should not be. Laws against discrimination are frequently passed retroactively, after society has (largely) changed its views, and the added burden of legislation does more harm than anything else. Disabled people had their highest rate of employment in the 2 years leading up to the passage of the Americans With Disabilities Act, with the rate dropping severly afterward.