The Republicans and Rove want to run against Hillary since they know she will lose the election.  The L.A. Times reports that the recent GOP attacks against Hillary are designed to raise her profile and help her win the nomination, so they can beat her in the general election. It's the same strategy they used against John Kerry in 2004. From the L.A. Times story:

The ploy was described by Rove lieutenant Matthew Dowd during a postmortem conference on the 2004 election at Harvard University the month after Bush defeated Democratic Sen. John F. Kerry of Massachusetts.

In the run-up to the 2004 Democratic National Convention, when it was not yet clear who Bush's opponent would be that November, Rove and his aides had begun to fear that their most dangerous foe would be then-Sen. John Edwards of North Carolina.

With his Southern base, charismatic style and populist message, Edwards, they believed, could be a real threat to Bush's reelection.

But instead of attacking Edwards, Rove's team opened fire at Kerry.

Their thinking went like this, Dowd explained: Democrats, in a knee-jerk reaction to GOP attacks, would rally around Kerry, whom Rove considered a comparatively weak opponent, and make him the party's nominee. Thus Bush would be spared from confronting Edwards, the candidate Republican strategists actually feared most.

Unlike Kerry, who had been in public service for decades, Edwards was a political newcomer and lacked a long record that could be attacked. And, unlike former Vermont Gov. Howard Dean, who had been the front-runner but whose campaign was collapsing in Iowa, Edwards couldn't easily be painted as "nutty."

...Consider Dowd's own words: