Number one threat for Indiana would be tornado.
Number two is earthquake. Many people don't know much about the New Madrid fault line and the danger it poses us here in Indiana.
I agree that, by far, the most common threat is tornadoes. We have several every year. However, while they are horrible for those directly hit, they are a very localized event. A quarter mile wide, and a couple of miles long is typically the extent of major damage. Go a mile in any direction from it, and there is power, normal traffic, society, and open businesses.
On the other hand, an earthquake could devastate many square miles of the state, completely disrupt all infrastructure over a wide area, and result in such a wide area requiring SAR that people could be trapped for days.
I must say that, of all the natural events, an earthquake ranks #1 on my scale. For example, I can picture one happening while I am at work. I don't spend much time in my office, so I may, if I survive, have only my dressy work clothes on, and my pocket pistol. No coat, gloves, hat, etc. I work downtown, and park in an underground parking garage, which would likely collapse, making my car unreachable, so I would be without my emergency supplies. I would have a 10 mile hike to get home, and supplied as I would be, there exist many scenarios that make such a trip doubtful (weather being a prime one).
I've tried to figure out how to prepare for such an event, and really haven't come up with much.
Civil unrest comes second. While I could at least get my coat, I would still be in the heart of downtown ill-equipped to deal with it.