The Ireland manager avoided the sack after last month's double-header with Germany and the Faroe Islands, but the experienced Stoke midfielder is unsure if the storm has passed and feels that senior players also have to justify their positions.
"If we lose against Greece and the performance is not right, I'm sure it'll be brought back up again and things will be said," said Whelan, when asked if it was nice to have the manager's future resolved after the Faroes victory. "And, on that part, we've got a couple of points to prove."
The 28-year-old has been a regular in the Ireland set-up under Trapattoni, but stressed that managers can come and go in football. "I've no real say in who the manager is going to be or if he should stay or not," he continued.
"It's nice for the FAI to back him and hopefully he can get on with the job. It's obviously difficult because we're going through a bit of a sticky patch and people's heads are on the line."
Whelan added that he was still smarting from Ireland's Euro 2012 disappointment, and thinks that the humbling experience in Poland delivered a dent to the squad's confidence which they have not fully recovered from.
Earlier, Marco Tardelli claimed that 2012 had been "fantastic" for Irish football, asserting that anyone who doubts the managerial prowess of Trapattoni is "not normal".
The Ireland assistant believes that it has been a good year because of the squad changes since Poland which have allowed some younger players some time to shine.
"For me, it's been a fantastic year," he insisted. "We go to play for the European Championship, that was very important for us. It had been 25 years since the Irish team had qualified.
"We discovered many players, many young players and I think when you have big change then it's important to have patience because we know that if the younger players go on the pitch it's possible to play very well one time, two times, very bad but that's football, we know football."
Tardelli mounted a strong defence of his boss, and suggested that people need to step back and put his achievements in Ireland into context.
"I think that (anyone) who thinks Giovanni is not a good manager is not normal," he continued.
"Giovanni, I think, is the best in the world with the journalists, with the board, with the players. I think after the Faroes, he showed everyone that he's a very good man for everything.
"I think you prefer to write that Giovanni is not good or that the players do not deserve to stay on pitch. But I'd like to read a detailed analysis of what Giovanni has achieved here. You can then decide if he's worked well or not.
"Giovanni did not have to defend himself. He spoke with the federation through John Delaney, not with the board. He spoke with him to see what happened."
Tardelli blamed the absence of senior players for the drubbing at the hands of the Germans, and backed the manager's stance with regard to attending games in England; the FAI encouraged the 73-year-old to travel more frequently, but his number two feels they already have the right balance.
"I think every week and during the week I go to see matches," he said, "Before, Giovanni stayed at home to see DVDs and things went very well. Did it work? It worked. Why do we need to change? Change? No problem, but why?"