The 13 Premier League clubs in the fourth round made 98 changes to their line-ups, an average of 7.5 per team.
Championship sides facing lower-league opposition also rotated players, with Leeds making 10 changes, while Brighton and Newcastle made nine.
"Clubs care about money while fans care about trophies. That's very unfortunate," Shearer told BBC Sport.
"It's just crazy, I don't understand it. I'm all for bringing kids into the team but not seven or eight of them. Six rounds from the third round to the final, it's not asking a lot is it?"
The rotation of players in the cup competition proved a talking point as Liverpool made nine changes and were beaten at Anfield by Wolverhampton Wanderers.
On Sunday, Premier League sides Hull and Watford both rotated their squads and were knocked out by Championship Fulham and League One Millwall respectively, while an unfamiliar-looking Leeds were eliminated by non-league Sutton.
However, seven top-flight sides who made five or more changes to their starting line-ups did make it through to the last 16.
On Twitter, Match of the Day presenter Gary Lineker said Liverpool boss Jurgen Klopp showed a "lack of knowledge of the depth in English football and respect".
Match of the Day pundit Phil Neville believes the changes are "making the FA Cup better", adding: "It's been fantastic to see the upsets so far. Jurgen Klopp has to find out about those kids. He has a massive academy. If you don't play them, you don't know."
Premier League sides have made an average 2.06 changes to their side from one league fixture to the next this season, a much lower figure than the average of 7.5 made over the FA Cup fourth-round weekend.
But 14 clubs from the top tier are scheduled to play again in the league on Tuesday, with the remaining six in action 24 hours later.
Southampton boss Claude Puel - who made 10 changes in defeat at Arsenal - said he would "do the same again".
Watford's Walter Mazzarri  - who made seven changes for the loss at Millwall - said he was "sorry" and referenced a focus on Tuesday's Premier League trip to Arsenal, adding: "I want a team that in the next 16 games fights for every ball."
But former Arsenal striker Ian Wright said he could not understand Mazzarri's move, with Watford 14th in the league. "I don't know what else they are playing for," said Wright.
After defeat at non-league Sutton United, Leeds United boss Garry Monk admitted his rotation "backfired" as he kept an eye on getting the "balance right" for Wednesday's Championship fixture at Blackburn.
There are now just seven Premier League teams guaranteed a fifth-round spot, while Leicester will contest a replay with Derby. At this stage in 2015-16 and 2014-15, 10 were left in the competition.
Managers often like to use the line that "we take each game as it comes".
But as the season enters February, with key fixtures, a busy Easter period and league run-ins on the horizon, it seems many of them are looking to future obligations.
Is FA Cup success deemed enough of a reward? The winners will pick up £3.4m if all prize money for wins from round three through to success in a Wembley final is added together.
By comparison, the difference in finishing a single Premier League place higher this season is expected to be £2m. Reaching the Champions League places is worth close to £11m and that is before taking into account television revenue and prize money for group stage points.
It would be unfair to cite finance as a pure motivation for squad rotation, though ultimately it forms part of the reward managers are aiming for.
Increasing recovery time for players is often central to the reasoning managers give for ringing the changes but former England captain Shearer claims he never got tired.
When asked on Twitter if the game was quicker and hence more tiring for players, Shearer replied: "They now have better diets, training and preparation. So shouldn't they be able to play more?"
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Clubs making wholesale changes are "cheating fans" out of an FA Cup run, according to BBC pundit Alan Shearer.