The commander abilities are in the voting menu. CTRL+V, then 9 to vote for a commander. They are often used to buff players for a big push. Commanders also get more abilities to strike the enemy and turn the tide. They require Command points which gradually accumulate over time.
Some players act as commanders quite a lot, other not much. I will do it from time to time, especially if the harvester is in trouble, or the team looks ready for a big push.