I was recently told by the city of Rathdrum Idaho that in order to operate a home based FFL, I would have to go through a $600 conditional use permit process to get A recommendation from the zoning department to the city council to approve the business or not. This would require a public hearing and publishing a notice in the local paper and mailing all my neighbors to notify them of the hearing, etc,etc.
http://www.rathdrum.org/vertical/sites/%7BB217A04D-FA9D-403A-9D25-24962991B1D9%7D/uploads/conditional-use.pdf

But I'm wondering, Idaho has state preemption, and it states specifically: "(2)  Except as expressly authorized by state statute, no county, city, agency, board or any other political subdivision of this state may adopt or enforce any law, rule, regulation, or ordinance which regulates in any manner the sale, acquisition, transfer, ownership, possession, transportation, carrying or storage of firearms or any element relating to firearms and components thereof, including ammunition."

This is from Title 18, chapter 33.
http://legislature.idaho.gov/idstat/Title18/T18CH33SECT18-3302J.htm

My question is simple....how can the zoning department or city council prohibit me from getting a home based FFL? Why would one need to pay $600 to go through their process if it would be in direct conflict with the Idaho State law?

And how would I proceed as far as my FFL application goes?

It isn't the FFL that's the problem. You're attempting to run a business from a residential area. businesses have to comply with zoning rules.

Even if those zoning rules violate state preemption?
Doesn't make a lot of  sense

They aren't singling you out because it's a gun related business.
I'll bet if you rent a storefront and they'll have no issues granting you a business lic.

I'm sure your right but that's not my point. That's not what I want to do

I know they make people to through the same process to open a daycare....but there isn't anything in the state law that offers preemption for daycares

The state is not interfering with your firearms rights, since these stipulations apply to ANY business, not just to a firearms business.  But if you think your pre-emption argument has merit, hire an attorney and sue.

$20k will probably cover the initial suit, or you might find an attorney to handle it pro-bono for the press coverage.

(I posted with WA law, since you give your location as WA, but now see that you're asking about ID).
So, do you think zoning laws simply don't apply to FFLs, because preemption?  It would then follow that you should be able to open a busy, retail, storefront gun shop in the middle of a residential neighborhood, right?

In most states with preemption statutes, there's an explicit exception for generally-applicable zoning ordinances.  WA has such an exception.  I don't find one in ID, nor do I find any case law on the subject at all (for that matter, no case law dealing with preemption at all).  I suspect that, if you were to litigate the issue, the courts would still imply such an exception--localities can't have special zoning rules just for FFLs, but they'd still be able to hold them to the same standards as any other retail business.  I could be wrong, but that's my best guess.  I'd virtually guarantee, though, that if you won, the preemption law would be amended in a hurry to add that exception.