Neither is any minister in most democratic country. You don't get to vote for the Secretary of the Treasury or any member of the government directly in most systems. Presidential systems have an exception in the person of the president, who is personally elected, but everybody else is appointed and merely approved by the parliament.
In the European parliament, the EPP won the parliamentary elections last June, and they approved the nomination of the Von der Leyen Commission, like how the Starmer Cabinet got approved by the House after the Labour won the elections.
The real difference is that nobody really cares about the European parliamentary elections: in pretty much every country it works like some kind of intermediate election for national parties to assess their strength, and they don't really campaign as members of EPP or S&D and mostly as members of their own national body without any consideration for European politics. And that's quite a serious problem.
The EU has many institutional issues (most of them deriving from the fact that individual state leaders refuse to give more power to the EU), but the Commission members not being individually elected isn't one of them.
This is at best a difference of degrees. Neither the commissioners nor the civil servants have their names on a democratic ballot or are otherwise considered in any real way during the election process but both are indirectly chosen by the elected government. The question is how many degrees of separation do you need before the democratic elections no longer have an effect on the rulers chosen at the end - and the answer is probably not that many.