To be a Republican in NY, like much of the Northeast, is not like being a Republican in the rest of the country. The Northeast still favors "Rockefeller" Republicans, liberal on social issues, conservative on fiscal issues (well, what used to be known as fiscal conservatism in the pre-Regan and Bush days: controlled spending, a balanced budget). Over the last few decades, Rockefeller Republicans and the national Republican party have been moving further and further apart, and share few positions. The national party sees the Northeast as little more than a revenue source, with New York only receiving back $.85 of every $1 sent to Washington.
Since they have little in common, you would think that the Northeast Republicans wouldn't be assisting the Republicans in Washington. Mayor Bloomberg certainly does, and he is leading a new effort to ask New Yorkers to withhold contributions to politicians who do not support New York.
http://www.nytimes.com/2003/10/23/nyregion/23FUND.html
Bloomberg specifically mentions Tom Delay as the type of Republican who supports policies that hurt New York. Then the article goes on to point out that Pataki has recently hosted a $1,000 per person fundraiser for Tom Delay.
It seems Pataki cares a lot more about brown-nosing the national party for a job than his does about the state he was elected to serve.