As someone who worked in Public Affairs for a Federal Department for decades (most of it during Republican Administrations) let me break to you, the news industry does not show up on your door the day that everything runs smoothly. People don't tune in to any network news to hear that things are going as planned. Even Fox news trades on the negative, most of the time. Their focus is just distributed to topics of interest to their viewers. Their viewers want to hear negative things about other subjects and fewer stories about the president. This is the same policy that the Wall Street Journal, which is owned by the same guy who owns Fox, follows.
I read the Harvard Study you quote. If you had, you would know that the study was done on Trump's first hundred days by the Shorenstein Center on Media, Politics and Public Policy. It's findings were published March 18, 2017. So you got the date wrong. This is important because it shows that you are quoting someone else who misstated the numbers, and did not do so yourself.
The general conclusion that CNN and MSNBC have some sort of bias is not proved by these incorrect numbers. Negative stories on Fox News were 52%, not the number you reported. The study reported no numbers for MSNBC or NPR. CNN did 93% negative stories. But, the German Network ARD's coverage of Trump was 98%. On specific subjects Fox's coverage was closer to CNN's. For example, on Immigration, Fox New's coverage was 81% negative, and on health care it was 79% negative. If the subject was perceived as negative by the public, it would have been difficult for Fox to spin it positively.
There was one story that was covered about 4 to 1, positive to negative. That was the case for coverage of the president's response to Syria gassing its citizens. Trump authorized missile strikes against military targets in Syria. Traditionally, opposition politicians stand behind the president in such cases, which most of them did in this case. That story makes news, and provided opportunities for positive coverage.
I know you don't believe it, but the news media does not make up the news. Photos and video of crying babies behind bars do not elicit positive public reactions. Attacks on health care for the poor, is not a touchy-feely story. The people doing this report, judged subject,not packaging, in reaching positive versus negative conclusions. The difference was in how much time was given to negative stories.