I don't think it refers to the Bible, More a symolic and as explained in the lyrics, to refer to a bird, or person that doesn't fit in with the crowd, the other birds/people are jealous and feel threatened by it's difference, trying to force it to become more like them i.e 'desiring to lower it's standards. It pretty much relayes to things like racish, homophobia, all sorts of idioms where those who deviate from the 'norm' are 'great speckled birds' The ironic thing of course is that while it originally refers to religion, or believers in God, It's Religion that is the most Racist, phobic, divisive part of life