Actually, the new FCC proposals are not aimed at Christian broadcasters (without the capital b), but to your run-of-the-mill station that's owned by corporate broadcasters. Sure, it will affect them. This is a side effect of operating stations on public airwaves. They should be held accountable for doing so and if you read some of the documents provided in Gearbox's answer, you will see why.
I think that the government is probably being a little heavy-handed all at once, however all broadcasters do need to be accountable for all of their stations operating in the community of license, regardless of content or message.
I can see why Christian broadcasters are so upset. They are about to embark on a spending spree if these proposals are enacted. They would need to build studios for each and all transmitters in each and every city they operate in. They will be required to keep someone in studio at all times in case of disaster or emergency. If you were listening to your favorite Christian station and something happened in your community, you would want to know about, right. That way you can act on that information. It's something that's been in the sights of the FCC for a long time and the blackouts, disasters, weather events and other community oriented events that haven't been reported on by all broadcasters, especially in smaller markets is what it took for the FCC to pay attention. Many times, stations in smaller markets have not one person in the control room when a public emergency took place.
In short, it isn't about the programming, but about the community and the public and this is why these changes are being looked at by the FCC.
EDIT:
Perhaps no one does or maybe they do. This is why the Commission is taking public comments about the matter, to see if this is REALLY what the public wants or if it's just a few anti-corporate groups that have been less than approving about the lack of choice given to them.
As mentioned before, these proposals are in the works due in large part to the 20 biggest corporate broadcasters and not in any way because of religious groups.
From reading the documents, it would appear Christian broadcasters are paranoid that people with differing views will affect programming. While I am a in favor of the public being in control of public property, instead of the other way around, I will agree with the FCC in this proposal. I do not believe that Christian broadcasters should have anything to worry about as what I have read on the website is just speculation.
Even thought the proposals haven't passed and probably will not for quite some time, you should not really expect much in the change of the programming, however if you suspect a change will affect the way you listen to programming, or if the programming is at all compromised, then you should consider getting the next best thing, satelitte radio. Satelitte radio, or SDARS, is not regulated the same way regular radio is, so chances are that you might find something that interests you. Of course, you can voice your opinion to the FCC in the way of making public comments as was mentioned by Gearbox.