Lousy customer service is inexcusable, but that is really not the issue. EWR has become such a quagmire of delays, that CO is doing everyone a disservice by booking ANY connection of less than one hour, much less showing them as a valid connection.
The OP learned a hard lesson that those of us who are slaves to connecting in EWR from smaller markets have also learned. I fly regularly from ORF (less than 500 mi) and only take a connection of less than 2 hours when the alternative is more than 3 hours. I don't even look at anything less than an hour.