There are multiple ways to deal with this:

1. Resetting the game:  If you have a browser strategy game then the players that have been playing since the start will always have a resource advantage, resetting the game every few months will allow new players to join in.

2. If you have some sort of travel time rules you can place players that have a similar join time close to each other. Typically this means placing the players who joined first in the centre and the newer players outwards works quite well.

3. Limiting who you can attack to only allow attacks against players of a similar level.

4. Making defense more effective then offense. This means that players in general are less inclined to attack one another. 

5. Allow players to construct something that prevents a constant number of resources from being stolen/lost upon being attacked. If I can prevent 100 of each resource from being stolen in an attack and I only have 100 resources then attacking me is not going to accomplish anything. A good player will likely skip this upgrade as they will quickly begin to dominate the local area. But a new player will be able to hide behind this building preventing him/her from being attacked.

6. Allow official alliances and let weak players give some sort of mechanical bonus towards being allied with a stronger player but make them lose a bit of this each time the weaker player is attacked. This should cause stronger players to protect their weaker allies. Maybe protectorate is a better name.