Hello!
There are rather fast, efficient and regular train connections linking Tallinn to neighboring towns. I suggest you to look on elron.ee, as well as peatus.ee to check which towns are well connected and how long it would take you to go to Tallinn. For instance, look at the stops on the line between Tallinn and Aegviidu or between Tallinn and Paldiski. Keila for instance is a small town to the West of Tallinn. It is quiet and close to the nature, and you have train connections to Tallinn almost every 10 minutes. It takes about 40 minutes for a train ride between Tallinn and Keila, so not more than if you were living in some neighborhoods of Tallinn far from the center.
If you can work from home, then it could be a very nice idea! And actually if you are drawn into nature, you could even make your life further away from Tallinn. Estonia is not so large, and transport network is good. You can also find shops with food and other basic needs outside of the capital.
Bare in mind however that there are less rental offers outside of cities. Many of the places you would find are for sale, not rent, and the ones for rent might not always be in as good conditions than you would find in cities. Good side is that renting is MUCH cheaper anywhere that is not in Tallinn.
Finally, if you want to live in Estonia and you don't care much about Tallinn, I suggest you to look at smaller towns. Locations such as Viljandi, Haapsalu, Kuressare are certainly attractive, close to nature, small (5000 to 15000 inhab.) but with easy access to all the facilities you would expect (shopping malls, hospital, etc.), with easy access to the rest of the country (except maybe for Kuressare, which is on an island), and with a larger choice of modern and equipped flat to rent than in villages around Tallinn.
I hope I have been helpful. I think it is a great idea, I like it a lot when people come to the Baltics for something else than the capital cities 
Don't hesitate to contact for more!
Nicolas
