Hi Chani, another Larry here chiming in with two words: yes, and yes!
Yes, it can be a time-consuming hassle to travel from town to town by public transport, but there seem to be various train schedules throughout the day that will get you from Bologna to Assisi with just one change in Firenze, meaning no stairs. And while you would then need a taxi into the town of Assisi, the taxi should be able to deliver you right to the door of your lodging, making things considerably easier and quicker.
And definitely another YES, Assisi is so worth the time and hassle to visit. It is a wonderful very old and historic town, with many sites, especially beautiful and very old churches, endless ancient residential lanes, and shops that are often a cut above the norm in popular hill towns. The Rick Steves walking tour, you can download it to your phone or tablet, offers a great walk through the whole town, although I'll warn you to pay especially close attention to getting on the right track at the beginning of the tour, with a map in hand, as I got off-track at the outset, costing me considerable time, and others told me they did too. There are many varied churches throughout the town, culminating at the Basilica di San Francisco at the lowest point in town, actually two basilicas, the upper and lower. I found the lower and smaller one to be especially beautiful, intimate and moving. The RS downloaded tours of the Basilicas were great too. I only wish that I had had more time in Assisi, also that it had not started raining when I got to the Basilica(s), although early evening as the rain wound down was special too.
If you can manage to visit the large church in the lower town near the train station, that is lovely and significant too. Without checking, I think that is the one that contains the tiny chapel where St. Francis began his ministry.
Enjoy your trip Chani, and let us know how you find Assisi. Shalom, Larry