It's not ignoring Johnston's faults, Johnston had many faults, but in the end he was just one general. It wasn't his job to curtail and bow his head to Davis, to sweet talk the President into getting what he wanted, it was his job to command in the field to the best of his abilities - which he may or may not have done - and given a high profile job he should expect to get the President's total support but he never gets it because Davis will not give it to someone he doesn't like.
Davis is the Commander in Chief, it is Davis' job to assess his subordinates, understand their different plus and minus points and deal with them differently to get the best out of them, he fails completely at this. If someone does not either kiss his arse or treat him in a friendly and respectful manner he doesn't have time for them and will not offer them any support.
If it were Johnston's fault that was the major point in this then in OTL it would have been only Johnston who had troubles with the Government but in OTL Beauregard, Chase Whiting, W.H.C. Whiting, Mansfield Lovell, Leonidas Polk, William J. Hardee, John C. Pemberton, D.H. Hill, John Magruder, Benjamin Huger and many others, sometimes including Braxton Bragg, all had trouble with the government and the President.
Had John C. Breckenridge been the Commander in Chief he would have been much better at dealing with people because he, far more than Davis ever did, understood that nobody was the same and everybody had to be treated differently, that's partly why his period as Secretary of War went so well.
Impressive in appearance and bearing and good with words Davis may have been but he had no people skills and that major flaw destroyed the working relationship between many generals and the government. If I had to pick one major difference between him and Lincoln it would be this.