While I can understand the annoyance at this making things harder for them there is an underlying sense of entitlement in this article. And it starts in the third paragraph:
"Neither company has officially told us that we’ve been cut off. For a time, it was possible to make a good-faith assumption that this was just a short-term disagreement. Maybe their spam filters were misplacing our emails. Maybe they’d get over it. Or perhaps they feared a repeat of 2007, when then-Kotaku editor-in-chief Brian Crecente embarrassed Sony out of blacklisting this outlet for reporting the existence of then-unannounced PlayStation projects."(Hyperlink removed)
Essentially, Totilo wants to be able to write whatever stories he wants and still get the benefits of toeing the line like a good PR outlet. The problem is that it's not 2007, the rise of Let's Players or independent commentary from people like Totalbiscuit has put huge pressure on the "journalistic outlets" like Kotaku since game companies can get widespread coverage at a fraction of the cost.
And it's clear that they know this. Back in 2007 when the independent coverage was still in its infancy it was wise not to anger outlets like Kotaku. While the publishers had money to influence coverage the outlets still maintained some power since they were nominally independent of the publishers. In 2007 losing Kotaku coverage would have been terrible, in 2013? Not so much.
For the price of getting positive coverage from Kotaku, Bethesda and Ubisoft could potentially get far more from the Youtube creators.
All this means Totilo has a choice. It's publish what you want and face the ire of the publishers and the consequences of their actions, or you can be a good little PR outlet and get all the help and support you want.
While the latter turns you into an untrustworthy shill, the former means you have to do more work in order to publish stories.
And that also seems to be what scares him.