This has no bearing on the legitimacy of the EU. Members of the commission are selected by the democratically elected government of their respective countries.
People that downplay the democratic legitimacy of the EU really, truly, unequivocally do not understand what they are talking about or have a malicious intention.
People vote for their national parliament. Parliament appoints a government. Those appointed governments then discuss who to appoint in the commission. Europarliament gets a say, but can only accept or reject the entire commission, not specific members in it.
The Europarliament is the only democratically elected body on the EU level, and its power is sorely lacking.
I understand why people say this. The population have not directly voted for these commissioners. They can't simply vote them out. It feels like a step removed from the democratic process, and I'm not sure that's beneficial.