Using Kumamoto as a hub?

We'll be in Kyushu for a week and we're able to book a hotel with points for about 5 days or so in Kumamoto. Is it plausible to take day trips to the surrounding areas like Kagoshima or Nagasaki? We'll be on the jr pass. Are there any places that aren't reachable if we were to do this? Thanks.

Yes, it is possible if you do not mind seeing all these places just in daytrips. The train trips to Kagoshima, Nagasaki, Aso, Fukuoka and Kitakyushu are relatively short. However, if you go further than that, it start getting a little bit time-consuming. Also, in my opinion, many of Kyushu's best attractions are best enjoyed with an overnight stay, especially the onsen towns such as Kurokawa, Yufuin and Beppu.

I would like to add that places like Kirishima and the area about Mt Aso and the eastern coast requires an overnight stay.

Also the area south east like Miyazaki is too far to be visited as a day trip.