Before I buy that bridge, I'd want to you to be a lot more explicit about which parts of government, which parts of the media and on which issues. I haven't seen most of the media notably pro-Trump for example, to which I've no doubt you will say "ah yes, well Trump isn't the true government", or some-such.
Every single bit of government, with different parts of the press. No, Trump's not in bed with NPR... but it's hard to argue he's not closely involved with Fox personalities. Hannity showed up at Trump rallies and often chats to Trump via phone.
Every Congress member will have a variety of sympathetic press sources that match their politics. Every department has a press corps that depends pretty heavily on access to do their jobs. etc. etc.
Right, but IMO that's meaningfully different from "the government and the press are in bed", which implies a wholesale conspiracy.
The fact that individuals within government can find favourable coverage from one of dozens (hundreds?) of independent media outlets, each with its own perspective and bias, isn't really all that surprising or scandalous.
Trump asking the NYT to squash a corruption story about one of his Cabinet secretaries would likely fall flat, for sure.
Obama's CIA asking Fox to suppress a story about the impeding attack on Bin Laden would probably have been honored, regardless of Fox's generally negative opinions on Obama.
Stuff with the "national security" label, or stuff that requires fairly specialized access to sources, is where the close relationship between press and subject can cause issues like the article here is highlighting.