You may be interested in this site:
Start with the very first essay. If you find it interesting, move on to some of the others; they are quite informative.
At a basic level, the argument is still, "I don't understand how this could have evolved, so therefore there must be a creator guiding development." I'm supposed to be a hard-nosed skeptic concerning natural explanations, but then credulously entertain the possibility that there is some mysterious, unidentified something consciously guiding the molecules so a bacteria can move around? How do I get from not fully understanding the cause of a flagellum to positing a sentient super-being who guides bacteria bits around by some unknown method, through some unknown super-power, and for unknown reasons? Isn't "I don't know" a much more honest answer?
In the absence of conclusive evidence, I find it entirely reasonable to assume that the answer lies somewhere within the natural world, because that is a simpler, more plausible answer than this mysterious super-being that ID proponents are relying on.
If my socks go missing, it makes more sense to say that they are somewhere in my house than to posit a sock-gnome, or, worse, an unidentified sock-vanishing force. That I don't know where the socks are doesn't mean my naturalistic, "they're probably in my house somewhere" argument is invalid. It's an inherently more credible argument than any one invoking a supernatural cause. Someone bemoaning my naturalistic assumptions, concerned about the gaps in my theory, upset that I can't give a conclusive, step-by-step picture of where my socks went and how they got there, is still a silly ninny if they propose "an intelligent sock-vanishing theory." We would know right away that this person is an idiot. Sock-vanishing and flagella-development aren't the same, but the analogy is, I think, relatively sound. In each case the natural assumption is more reasonable, and positing a supernatural guiding super-duper something-or-other is pointless.