When the cuts were first proposed in 2001, McCain joined Democrats in voting against them. At the time, he said the tax breaks didn't do enough for the middle class, and because of a need for increased defense spending.
In 2003, the phased-in cuts of 2001 were accelerated but McCain again voted no, saying taxes shouldn't be cut in time of war. But in 2006, when the cuts were extended, McCain voted yes because he said opposing the extension of cuts already in place would amount to a tax increase.
Updated: This post has been updated to correct the reasons McCain gave at the time for opposing tax cuts in 2001. Our initial posting attributed his reasons to statements he made later about fiscal restraint.