How do I protect resources?

Any resources still in boxes (from rewards) that you see in yuoir items menu are safe. Any resoruces produced / gathered and stored in the warehouses (at the top of the screen) can be raided.

A depot protection level can be gained for the warehouses if you are a farmer class. As a farmer you will always have a good level of protection. But you are not as strong.

Certain alliance technologies can also be researched that will give all alliance members a level of protection (lower). This will depend on your alliance donating resources and building up the technology.