There are multiple ways to deal with this:
1 reseting the game, if you have a browser strategy game then the players that have been playing sinds 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.