The term isomer is a vague one. It also depends on the time scale that you are looking at. In the butane example, two different conformations of the molecule could be considered isomers on a very short time scale, however, in practical applications they can be considered homomers (the antonym of isomers).
With resonance structures, you're never looking at two isomerizing species, you are looking at two (or more) extreme possibilities for where the electrons are at. The reality is somewhere between the extremes (the resonance hybrid). If we were to try to change the time scale to be faster than an electron can move around, then we run into a quantum mechanical problem, but remember that in quantum mechanics you never see a single electron relative to a nucleus, it's always a probablity function for where the electron might be. You can't have a time scale fast enough to consider resonace structures to be isomers.