He was left in Command in Futures End, and made it look easy.
After that, Kim was relegated to comic relief.
"Command" is verbally given from one command officer to another on the bridge and can't be taken.
This doesn't make you Captain or Acting Captain.
You become acting Captain after your Captain dies, and you have the balls to take hir job.
In Workforce, Chakotay decided to treat Kim and ECH's opinion equally, as if they were squabbling siblings trying to get the car for Friday night off dad, which is a massive insult.