> ASSANGE encouraged sources to (i) circumvent legal safeguards on information; (ii) provide that protected information to WikiLeaks for public dissemination; and (iii) continue the pattern of illegally procuring and providing protected information to WikiLeaks for distribution to the public.
The main charge here is that Assange actively encouraged people to break the law. Since he wasn't a US citizen and had not signed a non-disclosure agreement with the United States, many of the laws protecting classified information do not apply to him directly.
The first section of the indictment describes the various ways in which Assange and/or Wikileaks said, more or less, "gee, it sure would be nice if someone got these classified documents for us." The next section, titled "B. Chelsea Manning Responded to ASSANGE'S Solicitation and Stole Classified Documents from the United States", explains how Assange's solicitation lead directly to the criminal acts committed by Manning.
Finally, we have a section labeled "C. ASSANGE Encouraged Manning to Continue Her Theft of Classified Documents and Agreed to Help Her Crack a Password Hash to a Military Computer". This described how Assange provided Chelsea Manning with tools allowing her to circumvent passwords and other protections on classified computers.
So this isn't as simple as "a journalist received classified information and is being prosecuted for it." This indictment lays out a very specific crime, which is (Assange) directly encouraging and enabling another individual (Manning) to commit a crime (Espionage) on his behalf.
You can argue about the validity of these charges, even the validity of the classifications levels assigned to some of the material given to Assange, but we should be clear about exactly what is being claimed by the government, as well.