It's quite a mix of multiple things...
For one, Japan is typically sided with the US in terms of International policies, especially in the area of carbon emission, animal protection, etc. This opposing stance generally does not jive well with the common Chinese citizen.
Two, with China's growth in population and economical power, natural resources such as oil and food becomes more and more of a dire issue. In turn, this means more aggressive approaches in terms of securing on water territory control for seafood (citizen-level) and underwater control for oil (gov/big business level.) One area of hot debate is the rights to Daioyu/Senkaku Island:
http://en.wikipedia.org/wiki/Senkaku_Islands and (a mess that the US government sort of left behind.)
Finally, politicians from both countries uses the nationalistic hatred to manipulate the people or dodge political issues. This is especially true for the Japanese nationalists, who wishes to expand their defense force into a more legitimized army. In their attempt to show "guts", they would purposely make war-denial statements, trying to justify war prostitution or commemorate "war heroes" (which is not a popular move with any of the East-Asian countries, not just China.) Unfortunately, this also feeds to some Chinese media who wants to play up this image. It's also a funny sight to see since the stance changes back and forth with each change of the Japanese prime minister/majority party.
There are also some other minor reasons such as the treatment of illegal thai/viet/chinese immigrant workers in China, political ploys of pro-independence Taiwanese politicians, Tuna market price gauging, intellectual property theft that goes both ways (foreign companies would also steal Chinese tech, since the intellectual property laws are so weak in the country.) etc.
Long story short...it's the typical nation to nation tension.