What do you mean that they taught you about the "inner workings of the atom" ? Did they teach you the probability density functions describing the position of electrons ? How much did they teach you about Quarks ? Or the w and z particles ?
Relativity doesn't go against evolution - but you weren't taught that, were you ?
And why should our not knowing how a particular system evolved - when there is virtually no direct evidence (all we have is modern organisms greatly removed from the organisms who evolved flagella) - be a serious problem for the truth of evolution anyway ?
Now I do suspect that Behe may have deliberately chosen to look at systems where the available evidence was very limited. After all if you are making an argument from ignorance then you want to look at systems we don't know too much about. But I won't say that that is what he did - even though I've got a better case than you have - because that case still isn't good enough.
This paper - currently unpublished - proposes an explanation of how a flagellum could have evolved
Evolution in (Brownian) space: a model for the origin of the bacterial flagellum
Do you think that you could have handled that in school ?