Archer was a member of the Rajasthan Royals team beaten by Gujarat Titans in the IPL qualifier last Friday and is not with England for the first Test against New Zealand at Lord's, starting Thursday.
The 31-year-old is now in Barbados, the country of his birth, and will not return to England until after the first Test. The second Test at the Oval begins on June 17th, and Archer could now miss that match as well.
Archer, however, still has an England central contract.
Former England captain Michael Atherton has labelled the situation incredibly frustrating, with Simon Doull, a former New Zealand paceman, branding the injury-prone express quick's absence from the series opener "absolutely ludicrous".
But Stokes, speaking to reporters at Lord's on Wednesday, said there were two sides to the story.
"I totally understand people's frustrations around it, but there is another side to it," he said.
"A lot of it has to do with the landscape of cricket and where it is at the moment.
"A lot of points people are making around Jof and that situation, are to do with the landscape when they were playing.
"But it's completely different now. There's opportunities for cricketers now that there was not 10, 15, 20 years ago.
"Yes, in an ideal situation, it would be unbelievably great to have everyone who you want available at every single opportunity.
"That is not the way of cricket at the moment. There is so much more out there for players."
Stokes said that no one should question Archer's desire to play for his country.
"There is a situation where it could get messy and players like Jofra might not play for England again if you handle it in a different way, and that is not good for anyone," he said.
"Jofra has shown that he's committed and loves playing for England. Just because he's not available for this first Test match does not change that."
