The European parliament works just like any other. Commissioner is synonymous with Minister. They are proposed by their member state and each state get to nominate a single commissioner. They are elected by the European Parliament, the body that is elected by the general populace. This is arguably more democratic than being apointed by the Prime Minsiter, where appointments are made because they are the PM's political buddy, in the way they are in the UK.
Paliament members vote on issues and elect the President, Vice Presidents and Commissions on behalf of the people that elected them. This is literally how parliamentary systems work.
The people that work in the Commission are civil servants, like the ones that work in Whitehall. They are unelected, again, like the ones in Whitehall. These are the people that write laws, and keep the wheels of government moving, in Whitehall's case, as slowly as possible - see Yes, (Prime)Minister.
Get back to us when you can vote directly for cabinet in your country. I'm betting you vote for parliament, just like the rest of us, and then that appoints a cabinet. Why should the EU be any different?
This is not new. For example, there are also no ministry election or, yet the government of the day still put people onto that position. This is just one example, if you're coming from the US, you can even think of the even more examples of non-directly elected official making important policies.
But judging by your two comments here, you have given this matter very little thought.