In the case of Deep Throat he was revealing illegal activity, and doing nothing illegal himself. It was important that the press' right to keep confidential sources be protected so that Felt/Deep Throat would not face retribution against himself or his family for doing what was right and necessary.
In the Plame case the confidential source acted illegally revealing the identity of a covert CIA operative to the press as an act of political retribution against her husband.
The cases are as different as can be, one is an excellent example of the necessity to maintain the right to keep confidential sources, and the other was an illegal act that has nothing to do with protecting whistleblowers.
Bill Israel at Editor and Publisher outlines the case better than I can.
In this case, journalists as a community have been played for patsies by the president’s chief strategist, Karl Rove, and are enabling him to abuse the First Amendment, by their invoking it.
The problem, as always, in dealing with Rove, is establishing a clear chain of culpability. Rove once described himself as a die-hard Nixonite; he is, like the former president, both student and master of plausible deniability. (This past weekend, in confirming that Rove was indeed a source for Matthew Cooper, Rove's lawyer said his client "never knowingly disclosed classified information.") That is precisely why prosecutor Fitzgerald in this case must document the pattern of Rove’s behavior, whether journalists published, or not.
For in this case, Rove, improving on Macchiavelli, has bet that reporters won’t rat their relationship with the administration’s most important political source. How better for him to operate without constraint, or to camouflage breaking the law, than under the cover of journalists and journalism, protected by the First Amendment?
Karl Rove is in my experience with him the brightest and most affable of companions; perhaps I have been coopted, for I genuinely treasure his friendship. But neither charm nor political power should be permitted to subvert the First Amendment, which is intended to insure that reporters and citizens burrow fully and publicly into government, not insulate its players from felony, or reality.
Reporters with a gut fear of breaching confidential sources must fight like tigers to protect them. But neither reporters Cooper nor Miller, nor their publications, nor anyone in journalism should protect the behavior of Rove (or anyone else) through an undiscerning, blanket use of the First Amendment that weakens its protections by its gross misuse.
This is not a free speech issue, as free speech itself is compromised by reporters invoking it.