I don't understand this comment. Of course the airlines don't want you to check in your bags! It saves them money. Less chance of you requiring interaction with a check-in agent and far less chance (read: none) of the airline losing your bag in the first place! The airline doesn't really care how many bags you try to push through screening because that's TSA's responsibility.

As for the other part of your post, chaos at EWR check-in is extremely normal especially on a Thursday afternoon, one of the most heavily traveled days. Nothing new there.

-RM