The same reason some cd's are more expensive than others. New, more popular music may be more expensive than less popular music.
From a CNN article:
"Schiller said iTunes will now offer three price points for songs: 69 cents, 99 cents and $1.29. It will also offer all of the 10 million songs in its library without copy protection, and will allow iPhone users to download songs through 3G wireless networks.
In a press release accompanying the announcement, Apple said the pricing of a song will be based on what music labels charge. The labels that have agreed to the pricing include the four biggest - Universal Music Group, Sony BMG, Warner Music Group and EMI.
Many in the industry has been critical of Apple's 99-cent pricing, with some executives saying that it cut into profits on hit songs that could sell at a higher price"
http://money.cnn.com/2009/01/06/technology/macworld/index.htm?postversion=200901 0615