On the one hand, I fully believe that Answers in Genesis' new "museum" of creationist quackery in Kentucky (as if the south didn't have to deal with enough ignorant-hick stereotypes) ought to go down in flames as any monument to folly and ignorance should.
But I worry about the effect a formal protest will have, which, I think, will be next to none at all in terms of letting the public know about real science, and instead give Ham and his other little Hamsters plenty of material to work with in order to mount one of their famous "Oooo, the godless Nazi evilutionists don't want us around because they know we're telling the truth" lines of nonsense. Anyone who has ever dealt with creationists will know that they lie and lie and lie again, as if they are drawing from a bottomless well of rank dishonesty which is entirely justified, to them, by the belief they're saving people from their God's hell. Lies are to creationists as water is to fish. Even a court of law will not stem the tidal wave of their falsehoods, as the Dover trial proved.
Ham and his ilk have a common ancestor: P.T. Barnum. And this "museum" is little more than the present-day equivalent of the Cardiff Giant rolling tent show. Not only are there thousands of uneducated people who will lap up Ham's nonsense as eagerly as people lapped up the Giant hoax back in the 1800's, but they'll be all too eager to buy the conspiracy/persecution theories offered by Ham once supporters of real science allow themselves to be made angry and come out with signs. All Ham has to do is tell the flock that the protestors hate Jesus and are out to take away everybody's Bibles and turn their children gay, and the airlocks will slam shut on everyone's ears and minds.
I say if we're going to do this, is ought to be with mockery. (And maybe that's the protest's real plan.) Don't just stand around holding a sign. Go into the "museum," tour it, and ask the tour guides (if they have those) pointed scientific questions they won't be able to answer. Challenge them on their knowledge. Every time a creationist used to call the TV show when I was host, and claim to be very knowledgable about evolution, I'd ask him a simple Biology 101 question: what's the difference between a genotype and a phenotype? I never got a correct answer, and mostly got indignant huffing and puffing. (This isn't to say that no creationists know the answer, only the ones who called us.) The point is to let these people know that evolutionary biology is a vast field of science they just don't know. And that actually knowing facts should not be a scary thing. Remember the myth of Eden: the tree Eve ate the fruit from was all together now the Tree of Knowledge. That myth is at the root of all fundamentalist antiscience right down to the present day. Reality must be denied in favor of "faith," because that's what keeps the sheep in line and the collection plates full. Knowledge = bad = going to hell, Belief = virtue = going to Heaven.
That's a seriously emotionally powerful meme to have to overcome with, you know, boring stuff like evidence.
I think it'd be a good exercise to come up with funny ways to demolish the "museum" with satire, and then submit those ideas to people actually planning to attend the protest. If our side is shown to be confident in the facts, rather than being scared of a potential threat to "Darwinist dogma" (because remember, that's always how the creationists frame it), then a good dose of sarcasm and wit will go much further than you'd think. Jon Stewart and Stephen Colbert and South Park hit bullseyes as often as they do for a reason. Their way of treating things that are stupid really works. We ought to model after their example.