I agree that identifying and understanding the presuppositions of one's views aren't really important if you are doing science. Science is a useful way of understanding the material world, and the presuppositions don't really matter to the result of a science experiment, for example. The problem I see, however, is when those presuppositions bleed over outside of their proper sphere (i.e., doing science) and into realms they aren't suited for, like answering philosophical questions like "is there a god?" or " how should I live my life?" In that situation, the unexamined presuppositions predetermine the answer. For someone who wants to be intellectually rigorous, I would think this is a major problem.
The underlying issue here is that you and many others believe that there is stuff beyond the material world that we exist in. That is a presupposition too. It is unchallengeable because there is no way to prove it. That is, in my opinion, not really worth arguing about because there is no end to that argument.
Most scientist, even the Atheist ones, don't care about religion until the religion interferes with the progress of science and the accumulation of knowledge about the material world. Once your religion starts telling me that Global Warming doesn't matter because God has a plan, then I need to see some proof.