There are many reasons that all of your villagers can die, but the most common one is that they ran out of food and starved. You need to help them find new food sources as the game progresses by earning tech points, purchasing village tech and solving puzzles.

If you're new to Virtual Villagers, you should either use the option to get help the first time or read the Strategy Guide, so that you know how to take care of the villagers and keep them healthy.