I just got a call about this same issue yesterday. Admittedly, I'm not an Apple guy.
Customer was trying to use their iPad message app over HughesNet and it wasn't working. I thought they were referring to a standard cellular phone SMS message function, and not an Internet-based app, but now I see that may have been in error. I asked her to bring the phone into our office, so I may know more next week if she does.
Some programs interpret the higher latency over satellite as a disconnect and get trapped into an endless reconnect loop. This app may be one of them and simply may not work over a satellite Internet connection.
It's not clear from your message, but was this app working for you before over your HughesNet connection and then it stopped working?