If people are claiming the rationality tagline is code for transhumanism and technophilia, why wouldn't they also claim that for a more savory tagline?
I believe the reasoning is: savoriness of tagline -> unconscious gut-assessment of site legitimacy -> choice of side to rationalize.
Concerning Less Wrong's tagline, consider this plausible reaction of someone looking at LW for the first time:
And here are two real quotes from 2009:
And in reply:
The quoted text speaks for itself really. So therefore I think LW's admins/web designers should seriously consider replacing the rationality tagline with something more savory.