Pop didn't seem too concerned about Tony's feelings or ego during the first several years in the league when he routinely screamed in his face, gesticulated wildly at him during most every time out, benched him when he wanted to bench him and was so verbally abusive to him that the national media started referring to TP as "Pop's whipping boy".
I think some folks on here weren't fans in those years to know the history between Pop and TP. Essentially, Pop abused TP until TP began to think and act like the pg that Pop always wanted to be himself. TP is the creation of Popovich. Pop molded him and tore him apart and put him back together repeatedly until TP did exactly what Pop wanted whenever Pop wanted it.
When Pop wanted TP to be a pg that just brought the ball up the court and gave it to "Teemy", that is what TP did. Those were the days of the offensive set that was "Four down" every time down court. Then, when TD's legs got bad enough, Pop told TP to bring the ball up and start a motion offense that allowed TD to essentially remain in one basic position while TP ran the loop play and TD examined the defensive set to see what the best play was going to be. That offense was interspersed with the Duncan/TP pick and roll and the Parker drive to the basket.
In other words, TP has always done what Pop wanted him to do or Pop sat him down.
The only player that Pop has EVER shown deference to was Tim. No player before or since TD has ever gotten (or deserved) what passes for kid-glove treatment from Pop (though what passes for kid-glove treatment from Pop is less like a kid-glove than it is for any other coach in the league). Even Danny Green on his worst days has not begun to scratch the surface of abuse that TP used to get from Pop virtually every night. The abuse stopped when TP knew what Pop wanted as well or better than Pop did.
Pop doesn't scream at TP as often as he used to because TP earned Pop's respect. If he fails to do what Pop wants, I think we can rest assured that Pop will do whatever it takes to keep Tim as happy as possible, including screaming, benching, or trading anyone else on the team. If Pop is still coaching and TP is playing, it is because Pop wants it that way. And Pop only wants what Tim wants.
Doesn't mean there isn't a sense of loyalty between Pop and TP. Just means that the the sense of loyalty between Pop and TD is the first and last loyalty.