If you are referring to refugees who enter through those two countries, you are ignoring that these countries are also not initial ports of entry into the Schengen Area.
But I generally refuse to follow that line of argumentation: Having the initial ports of entry bear the responsibility for all new refugees is only a fair thing when you are not one of them. Neither Greece nor Italy have the capacity and as long as we are playing hardball international politics in the countries refugees come from, we have to take responsibility for the results of our actions.
http://news.sky.com/story/1557225/refugee-its-germany-or-not...
Now, suppose you are a refugee, a mechanical engineer fluent in Arabic and professionally competent in English.
Would you have a preference for a country like Sweden or Germany where you are more likely to get a job with your skills? Or would you equally accept being told to move to some other "safe country" where there is high unemployment, little demand for mechanical engineering jobs, and few English speakers?
How do you express that preference without your refugee status being questioned?