They're just like the civil service in the UK, or any other country. They do the bidding of our nationally elected governments. Nearly all proposals coming from the commission originate from the national governments.

So a law:

Starts with member states directly elected ministers pushing and agenda or the council (again elected) agreeing to push an agenda -> Commissioners take this agenda and work with it to propose law (using EU civil service like any other country does) -> The law then gets voted on by the EU directly elected ministers, who are meant to (and do) represent the people of the states more directly.

Everything in that step is as democratic as any other nation (or nearly).

Most people really don't understand the EU - and yes, it is confusing. This unfortunately makes it easy for certain interests to weaponise this misunderstanding. I've spent years (and years) explaining these concepts, but ultimately like any other argument, this is not a debate from logic, everyone has already made up their minds on emotion or ideology and nothing will make a difference.