score:6
Indeed Estonia has very few directs flights from anywhere and the situation has gone worse over the last couple of years. But there are a few alternatives which can make everything more fun, if you have time to travel.
For finding flights, as Karlson wrote, SkyScanner is your best friend. The chances that somebody will be able to tell you anything SkyScanner doesn't know, are very slim.
Upvote:5
There are multiple options available without the long layover from SkyScanner and Rome2Rio and those with long layovers in Moscow or Munich.
But I am sure that you can find something with a stopovers at other places St. Petersburg, Russia and then just take a train from there.