Multipool clients generally have two sets of functionality fail-over or load balancing. Fail-over is simply having backup servers in place so that your miner can continue working if your primary server goes down or experiences a connectivity issue. Load balancing will split up the work across multiple pools simultaneously. This would make the most sense to me in an environment where multiple people purchase a rather expensive mining rig and want to distribute shares of the rigs capability to accounts that are controlled by different owners. I can't see a scenario where this functionality could be unfair to someone mining in a single pool.