No issue whatsoever -- their gates are close at Indy and all gates are within the same security. A 45 minute connection has some danger at any station, of course. But IND is as well as anyplace.

If your HOU-IND flight is running late make sure the agent knows your concern, especially if booked these as two separate itineraries. They may be able to reroute you another way to get you to Newark another way.