EU commissioners are appointed by member governments, in much the same way that civil servants are appointed by politicians. In most democracies there are three pillars of government, legislative, executive and judicial. Commissioners are a part of the executive. And here lies the difference, the amount of decision making power in the hands of executive vs the legislative, and whether the members of the executive need to be directly elected vs indirectly elected.

You could also make the case that representative democracies aren't as good as direct democracies because citizens don't get to vote on laws directly.

Obviously there are trade offs between having elected heads of the executive who are more directly accountable to the citizenry but have less subject matter knowledge vs indirectly elected executive who have somewhat less accountability but more knowledge. There is also the case of less corruption because the indirectly elected heads of the executive aren't as beholden to special interests. Which I personally feel is a huge benefit.