How can I protect my resources during an attack?

As a trader you have no default protection although if you are in an alliance then the right alliance tech research will give you some resource protection. Make sure you are in an alliance and they are actively donating and applying the alliance tech research. Being in an alliance and keeping close to stronger allies can help to put off attackers as well.

Other than that you will only be able to stop enemies taking resources by shielding, running (teleporting away) or not having any thing to take. Try to complete as many activities as you can and build up the resource storage in your inventory items (boxes) which are not in danger of being taken. Only use these when needed.

Try to keep upgrading and researching to use up the warehouse resources (top of the screen). You will also become stronger this way and harder to attack.