The first reason:
He had a very lucky season in 2002, where that excellent defense carried the team close to the finish line. Many folks honestly believed that he could only get better from there, and saw his coming as a golden opportunity to elevate ND's program.
It was fools gold. To put it bluntly, as you stated very well in your post, the offense was putrid. Willingham and Diedrick kept trying to run that castrated version of the West Coast Offense, and kept trying to make square pegs fit in round holes to a much greater degree than Brian Kelly ever did. Seriously, trying to turn Carlyle Holliday into a dropback, West Coast Offense, short precision passing QB was stupid at best, especially since he had Jared Clark on the team for most of his time. It was all too easy for teams to simply run a zone blitz, and Holliday's inability to make pass protection adjustments as well as reading open receivers would stall many a drive.
The second reason:
He wasn't Bob Davie. Everyone wanted his head on a stick so badly, that we were willing to accept just about anyone, especially after the George O'Leary misstep. For the record, I think O'Leary would have done a very good job here, if given the chance.
The third reason:
He was the first Black head coach at Notre Dame, and many people were willing to cut him more slack, simply because of political correctness and not wanting to besmirch the first "African-American Notre Dame Head Football Coach."
A lot of his incompetence was overlooked that should have gotten him fired after that second year. The mainstream media kept propping him up, constantly spewing in our faces that he was the "2002 Coach of the Year" and that he got a 10 win season that year, and that he was a "molder of men."
Folks were willing to overlook the glaring warning signs in 2003, where that 5-7 season, by all rights, should have been a 3-9 season. We got extremely lucky against Washington State, as well as against Navy, as well as the Pitt game. For that matter, we could easily have gone 2-10 if it weren't for the heroics of Julius Jones having a fine season. This was a team that still had a pretty good depth chart, despite losing all of those NFL picks on defense from the last season.
Too many people said "Oh, he just needs to let his guys come in and play, and it will get better."
They were willing to overlook the fact that during the 2003 season, that his laziness in recruiting resulted in the worst recruiting class of all time (that awful class of 2004), where only about a half dozen players from that putrid class saw any meaningful playing time. While Darius Walker and Maurice Crum turned out to be multi-year starters, and Terrail Lambert did manage to make a few nice plays, the rest of that class was nothing more than scraps that very few Division Ia schools wanted. Seriously, Tregg Duerson? The two star player that no Division 1a team wanted.
Despite all of his gross incompetence, he was actually given an offer to stick around as the head coach, and all he had to do was terminate that good for nothing offensive coordinator, Bill Diedrick. Thankfully, he refused to do so and got fired.
By the way, does everyone here remember the mainstream media gleefully torching us after he got fired, especially how so many people screamed "RACISM!" after that fool was terminated?