The level of football. Say for example, theoretically if they took out countries like Russia or Sweden, and replaced them with teams like Lebannon and Saudi Arabia, the quality of football would be lower.
Also not forgetting that UEFA has 53 members, AFC has 47 and CAF has 56. CONMEBOL only has 10 members, but 4 of the teams automatically qualify for the World Cup, with one going into a continental play-off. So that's 50% of the teams potentially qualifying for the World Cup. In 2014 it may be over 50%, with Brazil being hosts. Again that's because strength of the South American teams is high.
It's a good point you make about people. But another point may be, how many of those participate in football in those countires? If more people participated in those big countries, their national teams would likely be stronger and FIFA would eventually have to award more places if it meant clearly strong footballing nations were missing out on the World Cup because there weren't enough qualifying places.
The teams represent their national football associations and i don't think the size of the countries really comes into it, they're all equal before matches are played and won, plus their ranking which is calculated by their results.
So in any case, i don't think any decisions will made by taking into account the size of countries or population. But more to do with how many members each governing body has and the strength of the teams, probably more so to do with the latter.