The bags aren't NECESSARY but they are NICE to have for a couple of reasons.
1) Often they have small wheels on one edge and a shoulder strap or pull handle. This makes lugging that thing to the check in counter much easier (especially since you'll also have a small child and your other bags in tow).
2) While the bags are soft so don't protect it from getting thrown around... your child actually has to SIT on that thing, so keeping it insulated from the dirt, debris, water drips, etc. of the tarmac is a nice idea (not to mention the stuff that might spill from other peoples' bags).
Also, if you're purchasing a seat for your child (which seems like you are unless you just have a large baby), you may as well bring the seat along and let him/her ride in it on the plane. Beware though, when installed forward facing, my son could feel the buckle behind his seat and it caused him pain, so make sure you get the buckle outside of the seat.
HTH
T.