I looked into this when I bought my 3ltr bottle for topping up while out in the field.
First of all there is no rubber boots for 3ltr bottles, so you can not stand them upright <img src="http://jsramsbottom.co.uk/bbs/e/icon_confused.gif" alt="Confused" width="15" height="22"><!--graemlin:-->, secondly divers use 3ltr bottles on sides of their big bottles for emergencies etc. so there are small canvas/strong fabric bags which will fit and have attachment clips/webbing to big bottles (this is the one I bought) it is not very protective, but for extra protection (dont laugh <img src="http://jsramsbottom.co.uk/bbs/e/icon_wink.gif" alt="Wink" width="15" height="15"><!--graemlin:-->) I put a couple of old sport socks (clean!) on it <img src="http://jsramsbottom.co.uk/bbs/e/icon_smile.gif" alt="Smile" width="15" height="15"><!--graemlin:-->. I think Daystate do a some sort of a (neoprene?) cover, but I went for the cheap, but effective option.
Nurek.