Sorry you lost your base, but this is how the game works. The longer you spend at your base, the more likely you'll experience raids. It's something like every 46 minutes you'll run the risk of a visit from your friendly neighbourhood mobs. But you learn how to protect yourself from them. Dig ditches around your base area but don't build within a troll's swing of the ditch because you'll lose stuff. They work a treat to keep 90% of the raids away.

Just in case you didn't know, hitting escape to bring the game menu up properly pauses the game now so you can AFK safely.