I agree with you. Why should Assange be prosecuted if the NYT publishers aren't? It seems a little hypocritical. Assange is taking all the heat but the MSM whores are the ones making the money off of the leaks.
You both may or may not be old enough to remember the landmark legal case, New York Times Co. v. United States, 403 U.S. 713 (1971). That case, which was brought over the publication of the so-called "Pentagon Papers", was litigated by a guy named Floyd Abrams. Abrams has become arguably the preeminent authority on First Amendment cases. He is an unfailing champion of speech.
Last week, he spoke to NPR and explained why this case is different, and why Assange is in some legal peril, and because of his conduct after the fact, he's increasing his exposure to criminal proseuction under the Espionage Act of 1917. The interview with NPR, may be found here.
Beyond what Abrams explains, and perhaps more directly to your point(s), this particular case differs from the previous New York Times or New Yorker cases in no small part do to Assange's possible involvement before the data breach occurred. Some have alleged (although the government has remained fairly closed-lip about their case), that Assange, either directly or acting through an intermediary, supplied material support to Manning, perhaps before during and after he stole that the classified materials.
That is going beyond just the purview of a publisher. That is acting as a co-conspirator, possibly.