1,000 years ago science could not explain lightning, does that mean that back then it was really Thor battling ice giants? Just because science can't explain something today doesn't mean that no possible explaination exists. Many of the predictions made by Einstein's theory of relativity would have to wait decades after his death until scientists & engineers could invent equipment with which to run certain experiments.
Science is an iterative process; each succesive generation stands on the discoveries of previous ones. Yes, science has been wrong before. The fact that scientists admit this is proof of the scientific method being applied properly; otherwise scientists would shoehorn evidence into models or lie outright in attempts to "prove" faulty models. But good science corrects its mistakes and either alters theoretical models (evolution) or scraps them altogether (aether).
And yes, evolution is "just a theory"; but then electron flow is also "just a theory", one upon which the computer or smartphone you are now using is based.