Well, vaguely, you could say it's sort of measuring how much the two functions are "in synch" with each other, much as the ordinary dot product measures how much two vectors are "in synch" with each other. The dot product of vectors can be interpreted as projecting one vector onto the other and then multiplying the length of the the projection with the length of the vector being projected to. So, in some sense, it's measuring how much one vector points in the direction of the other, with longer vectors being given more weight.
What you really need to get an intuition for is not so much the inner product, but the function space--the idea that functions can be thought of as some sort of vectors because an inner product is something you do to vectors. One way to say it is that functions can be added and multiplied by scalars. Roughly, speaking vectors are things that can be added together and multiplied by scalars. That's probably a bit unsatisfying, though.
One thing that might be a little more satisfying is the realization that if you look at a finite vector subspace of the space of functions, you get the vector subspaces that we know and love, namely R^n. Remembering that we are thinking of functions as vectors, we could take the the span, that is all linear combinations, of the functions, 1, x, and x^2. We get all the second degree (or lower) polynomials. There are 3 parameters, so it is a 3-dimensional space. So, it's R^3, a vector space we know and love.
As another example, you could take the interval from 0 to 1, divide it into n pieces, and consider all the functions that are constant on each piece. We get R^n.
Well, I'm getting tired, but if you keep thinking along those lines, you'll see how the inner product of functions is related to the one in R^n. Just think of doing a discrete approximation.