And it seems to be yet another "I don't know if I'm ready for this command" thing that so many fanfilms do.
Here I thought that they give commands and promotions to people who demonstrate confidence in themselves and their abilities.
You could well be right, its fair criticism. However to put it into context, this story arc is following on from Starship Ajax, (the Saladin-class Starship that was destroyed in the trailer). The Ajax series will act as a kind of prequel to Starship Challenger, although it is not part of the Anthology series. As the story goes, Colt was commander of the U.S.S. Ajax for 8 years until the ship was destroyed. She was an experienced and confident #1, but having lost her ship and crew, people whom she had known for years, it is to be expected that that such a person would take a knock in their confidence. This is the human equation and quite frankly if someone could just take command of another Starship straight after losing her previous ship and feel nothing, such a person would be a monster. It would be impossible for fans to be emotionally invested in such a character.