It used to be the case that the winner of the World Cup qualified automatically for the final stage of the following edition, but that's not the case anymore. France was the last team that this rule applied to, qualifying for 2002 by virtue of winning in 1998; afterwards, Brazil had to go through the regular qualification process for 2006 despite winning in 2002, and so did Italy for 2010, Spain for 2014, and now Germany for 2018.
What was the rationale for this rule change?
The main reason is to have more spots open for qualification. In 2002, before the start of the qualification, three countries were already qualified. These countries being France (1998 champions), Japan and South-Korea (hosts). So, only 29 spots were available for approximately 200 countries.
Closely related, in the 2002 qualification there were 14,5 spots for European teams, of which one was already assigned to 1998 world cup winner France. This caused other European teams to have a smaller chance of qualifying for the world cup. So, after the rule change, a nation is not affected in its qualifying chances anymore when a fellow confederation member won the previous world cup.
A minor reason could be to have the current world champion play more official matches.
