Kinnear was a controversial appointment by owner Mike Ashley in June last year, with the 67-year-old announcing his own arrival in a radio interview during which he got several of the players' names wrong.
His main role was to identify new talent for manager Alan Pardew but in his six-month tenure the club have signed just two players: strikers Loic Remy and Luuk De Jong, both on loan.
To compound matters, Newcastle lost influential midfielder Yohan Cabaye in the last transfer window, with the France international joining Paris St Germain for a fee believed to be around £20m.
Shearer, who replaced Kinnear as Newcastle manager after he was forced to step down due to ill-health in 2009, believes a combination of all these factors are likely to have led to the former Wimbledon boss' resignation.
"That's life at Newcastle United," he said.
"I shouldn't say I'm surprised but I was surprised in the first place when he was announced director, particularly the way the news was broken when Joe himself announced it on the radio when he got some of the players' names wrong.
"What has he been there now, about seven months? And two players have come in, albeit both players on loan.
"Maybe it's Newcastle's way of trying to say that the performance on Saturday wasn't good enough and why they didn't get any new players in, maybe that's one of the reasons.
"But they can only get players in if there's one man prepared to sign a chequebook."
He added: "You just never know what goes on at Newcastle behind closed doors.
"I think we were all surprised because Joe had been out of football for so long. Let's say that we hope he's okay and it's nothing to do with ill-health but it's just bizarre sometimes at Newcastle.
"Four, five weeks ago Newcastle were going so well, still in the FA Cup, Alan Pardew was getting manager of the month awards (and) they were looking up the league rather than finishing in mid-table.
"It's amazing what happens in three or four weeks in football, 3-0 on Saturday hurt everyone and they were second best all over the park on Saturday with a lack of fight and a lack of desire from the players and now it's come to this."