"His disciple cried impetuously 'but I believe in your cause and consider it so strong that I shall say everything, everything that I still have in my mind against it.'" The Gay Science 106
According to Heidegger, the scientific worldview represents the will to will, the will to power (so he says in the postscript to "What is Metaphysics?"). Of course, I think he's right, apart from not viewing this as a criticism of science. I also think, though I know it's controversial, that Nietzsche must have seen things that way. He's such a passionate seeker of truth, so committed to the cause of knowledge and science, that I can't see how he could possibly be interpreted as really rejecting all that. Rather, it seems clear that his criticisms of science and the pursuit of truth, frequent and harsh though they are, show something else. He thinks the project is just too important to be done wrong, so every tiny misstep must be ruthlessly exposed and obliterated. And really, criticism is essential to science.
Of course, it wouldn't do to take Nietzsche as an advocate of every cause he criticizes; I think it's easy to do so in the case of science and the pursuit of truth because he also so frequently praises those endeavors, and perhaps more to the point is constantly engaged in the quest for truth. But I wouldn't try to reinterpret his harsh criticism of Christianity as involving secret advocacy, for example, since he hardly ever has a kind word for Christianity and at no point seems to be trying to be a good Christian. On the surface, his attitude toward democracy seems to be closer to his attitude toward Christianity than it is to his attitude toward science. But is it really? He himself seems to see democracy and science as deeply intertwined, and after all he proudly proclaims himself a free spirit and a good European, aligning himself with people whose politics are pretty much exclusively liberal. And criticism is essential to democracy as well (and not to Christianity).
Thoughts inspired by teaching the first part of the Genealogy of Morals yesterday. Nietzsche says that all "higher natures" are a battleground between the master morality and the slave morality; surely he thought his own was a higher nature, but if there was any part of himself that was an advocate of slave morality, I find it much easier to believe that he felt a part of himself believing in democracy than that he had a Christian part.