Neelix is a very intelligent man 'in his own right'. Even though most or all the crew will sometime disagree. In almost all the eps. He doesn't really recognize the Federation or its principles but doting over the crew is something he does and he likes it.
In 'Fair Trade' season three Neelix expresses his absolute trust and gratitude in Capt. Janeway.
Just like if someone on this thread cared about it's topic.