Attacking the church is symbolically and literally attacking the community as a whole. It destroys the central social gathering place, the symbol of a people culture and causes harm to all its members. Its "churchiness" does make it more reprehensible an act than burning an empty warehouse or an individuals home.
Well, when the church actually represents that for a particular community, anyway. It's... not that clear cut, nowadays. Especially when areas where there's a... saturation, I guess, of churches. There's five or six within a 10 minute drive of my house. Maybe double that if you drive another 15 min. And that's only of the same religion
That kind of situation isn't uncommon in parts of the US, especially the less populated areas.
Intent would definitely be what would influence my reaction toward the arsonist, I guess. In this case, it was racism more than anything else. Symbolic (but perhaps not literal, or at least literal only regarding a subset of the community) attack on a social group, yeah. Hitting a school or valued non-Caucasian community member would be just as reprehensible (to me).
Of course, my most honest urge toward racists in general would be to burn every damn one of them until they stop breeding, but I obviously can't act on that. Logistics, at the very least, to say nothing of the legal or moral aspects. Some day, all those bastards will die. Might not be until the rest of the species does, but at least I'll be able to take that bright note with me. Though that's tiredness and ever simmering frustration (I live in/around a g'damn nest of bigots, and their shit wears on me.), not rational faculty (Which condemns bigotry in general as either hypocrisy or heresy, depending on the source. Re: Christianity, at least, intolerance/bigotry,
at all, is a direct violation of the teachings of Jesus and sin against their deity.)
[/rant], I guess.