This actually kinda makes sense, and the argument goes like this. It is rather obviously subjective what constitutes "promoting science and useful arts" (including the very definition of "useful" etc). So when it comes to enforcing this clause, you need some body to decide on what these translate to in practice. And this can be either the courts or the legislature. Between the two, the legislature is the one that citizens have more control over, so giving it the ability to decide is intended to make these kinds of abuses easier to rectify (just vote for the right guys!) as opposed to dealing with obstinate courts.
Let me assure you that you haven't discovered something hundreds of years of legal scholars didn't yet realize. You are simply mistaken as to how that clause is interpreted within the context of the rest of the document ... part of which outlines the division of roles and responsibilities for judging and executing that clause.
All of that aside, "science and useful arts" never referred to the little guys. This always referred to the interests of commercializing those endeavors.
