The cover command functions differently for each of the modes.
In ASSUALT mode, cover means "lay down cover fire here". For the sniper, Hume, it's a little different though, he should not lay down cover fire in assault mode, but stay in ready sniper position and take out any enemy he sees in the given direction.
In RECON mode cover means "watch this area and kill and engage and enemies that come in and are a threat". In this mode you will get a verbal report from your team first.