Allardyce made nine changes to his team for Tuesday's clash but was vindicated after second-half penalties from Matt Taylor and Jack Collison settled matters in West Ham's favour.
It was a hard-fought win against the Championship's table-toppers, which prompted Allardyce to criticise the questioning of his decision after playing a Premier League game just two days previously.
Allardyce said: "I can't see why everybody keeps moaning about changing the team - when it comes to cup competitions in midweek, when 25 are named, 25 are paid to play in the first team. Everybody seems to get on their high horse about it but we've been doing it for years and years.
"We played on Sunday, travelled back and got back at midnight, so it's ridiculous to think you'd send the same group of players up from Swansea to this game.
"Then they get injured and you come to Aston Villa on Saturday and you haven't got three or four of them because they've got injuries or fatigue, and then you lose.
"So you do your job and do it right, and whatever anybody else thinks doesn't matter."
The win came at a cost for West Ham, with James Tomkins picking up an injury and being replaced by Kevin Nolan in the second half, while goalscorer Taylor also picked up a knock.
"The only unfortunate thing is Matt Taylor at the end with a calf strain and James Tomkins with a slight hamstring but that's the price you pay," Allardyce added.
"We've already got too many injuries as it is. With Matt we'll be alright but let's hope James is."