it depends on the boot and the skirt...
a casual knee high skirt, with a utility boot (steel toe'd, or winterized like Uggs) do not go well at all. the smoothed natural silloette mixxed with more chaotic and synthetic look presented by the boots causes many asthetic conflicts and will often will make you turn heads for the wrong reason.
however the same skirt with a leather knee high boot... the smooth silloette of the hips and legs extends down to the feet making the person more asthetically pleasing. many people will find you pretty or sexy because the boots and skirt match so well. you will turn heads for all the right reasons.
so do boots go with skirts?
some boots do, but not all.