Save games were often deleted or wiped during updates.
Steam Cloud is now all up and running for the game, which should save your progress to the cloud from now on. So updates should now leave your save game intact.
Note for mobile / capped broadband:
Save games are less than 1-2kb. So don't worry about internet broadband usage if you're capped at a certain limit. Saving your game 1000 times would equal only 1-2mb in internet usage.