The Denmark international, who is set to lead his country out against England at Wembley next week, was hauled off just over an hour into Sunday's home win over Swansea.
He was not injured and had it been an attacking change there would have been no debate but his replacement was Kolo Toure, who has had his fair share of calamities at the back in recent weeks.
When the drama of the fluctuating 4-3 victory had subsided, questions over the reasons for Agger's substitution spiralled into more speculation about his longer-term prospects at Anfield.
However, Rodgers insists too much is being read into his tactical decision and said Agger would play against Southampton on Saturday.
"There has been a lot of spotlight, unfairly, on Daniel this week. What happened to Daniel was no different to what happened to any player," said the Reds boss.
"Just because it's a defender, it maybe gets highlighted a bit more, but we made the change and we won the game.
"It's no different to a winger coming off, or a striker or a midfield player.
"I don't judge players on the status of where they are in the group - it's what I think the game needs at a certain time.
"We made the change and Dan has taken it like the man he is.
"He has been outstanding in training this week and he will play on Saturday, no question about that."
The 29-year-old Dane has more than two years remaining on his contract but as one of the highest earners, having been at the club since January 2006, the prevailing wind at Anfield under owners Fenway Sports Group suggests he is one of those players likely to be in greater danger of being shepherded out of the door.
Goalkeeper Jose Reina, another significant earner, was loaned out to Napoli at the start of the season after Simon Mignolet was brought in from Sunderland on significantly lower wages while negotiations have not started over a new contract for England defender Glen Johnson, who has just over a year to run on his reported £110,000-a-week deal.
Agger has made just 10 league starts this season, having missed six matches in autumn after a freak gym injury, and with £16million summer signing Mamadou Sakho back in training after two months out with a hamstring injury Rodgers has another option at the back.
In line to face Agger at Wembley next week will be club colleagues Steven Gerrard, Daniel Sturridge, Johnson, Jordan Henderson and Raheem Sterling.
The latter two have played their way back into Roy Hodgson's squad with some impressive performances in the last couple of months and Rodgers believes the national team are the better for it.
"England have got a lot of good midfield players, a lot of outstanding players - and Jordan is up there among them," Rodgers told liverpoolfc.com.
"I was speaking with him earlier and he was analysing his game and areas he can improve with our analysts.
"He was then speaking to other people in terms of improving his performance.
"He's relentless that way. He wants to be the best he can be - and England is a better squad when Jordan is in it."
On Sterling, Rodgers added: "In the period since he came into the team, he's been outstanding.
"He's really grown as a young player - it's easy to forget he's still only 19 years of age.
"There's no doubt in his position that he's one of the best players in England.
"Over the course of these last few months you could argue there hasn't been anyone better than him in the England squad in that position.
"It's a great reward for him, his maturity and how he's approached the pressures of playing because he's played with a wonderful freedom and is working very hard for the team.
"He's very deserving of his opportunity."
Defensive midfielder Lucas Leiva has returned to training after a six-week absence with a knee injury but the trip to Southampton is too early for him to be involved.