Having the command channel open doesn't allow you to create new assignments/waypoints for free, it only lets you change which ships have which assignments. Come to think of it though, I don't know if the game ever actually tells you that.
It's kind of useless, though; it'd be cooler if every time it refreshed, you could
cancel an assignment and get your CP back.
I've lost count of the number of times when I've run out of CPs partially because of an assignment that I didn't even want to give in the first place, or which became moot shortly after issuing the command; fpr example, issuing a Strike command on a ship that's going to blow up in 10 seconds because its AI did something silly or a bunch of torpedoes got through is always a bit annoying.
The current CP system is probably one of my least-favorite things in the game, tbh, as it just puts a tight leash on using tactics unless you're going to put a lot of points into Logistics. It encourages hoarding of CPs, instead of spending them, which is irksome.
I really think it'd be more fun if, instead of limited CPs, there was a timer loop and putting more points into Command would shorten that timer, so that people who want to play the game like Starcraft can do it if they put lots of points into the Command tree, but even with zero points, people would be able to change fleet priorities over time. Then we wouldn't be able to set up Capture for every point immediately, but we'd be able to use things like Strike, which is pretty un-attractive when facing large fleets simply because of the CP wastage; it often makes more sense to simply designate a point where you want Strike stuff to concentrate, so that they won't just lay waste to one ship but will continue to scour that area.
Given how it works, I've resorted to deliberately "mining" for CPs sometimes by letting the AI capture points and then re-taking them just to get more CPs during really long battles; I am thinking seriously of writing the timer system as described above into Vacuum just to get rid of that issue, as it's possible to do