"I think the Assange/wikileaks indictment is a misstep by the justice department/current administration."

That is how power is gained, by taking risks. Maybe this will fail in court, maybe it won't. If it won't, the government will get more power.

"how can Assange be indicted but not the NYT?"

To demonstrate power, you don't need to be fair. In fact, not being fair is much more scary.

"I do think that Russia has made use of wikileaks"

To me, this begs a question, why was USA so inept in not making use of Wikileaks themselves? If it is an "independent" organization up for grabs.

Perhaps to get more power, you need a good enemy, too. That's why.