The home side took three points thanks to a goal from Charlie Adam in a game that passed without any major incident, although the opposing managers have aired their discontent with the tactics imposed on the game.
"I'm really disappointed we haven't won the game by more goals," Pulis told reporters.
"I think even looking at the first half and the chances; Robert Huth has missed a header from a corner Charlie Adam has had one he should score and Ryan Shawcross hits the bar when he is basically under the goal.
"I don't think they were bullied out of it, I think if you have a look at [Dimitar] Berbatov and a few of the others they are competitive enough, they can look after themselves.
"I think saying they've been bullied is unfair on us, we are strong and we are resilient but we are an honest group of lads that work hard. We are not dirty."
Adam scored the winner but Pulis was keen to heap praise on another former Liverpool man, with Peter Crouch receiving the plaudits from his manager.
He added: "We are structured and we are disciplined but we need him up there with Peter [Crouch]. If we get him up there Peter does a fantastic job for us and Charlie will get the opportunities to score.
"I thought everything we did today came through Peter."
Fulham have been disappointing away from home this season, and Martin Jol bemoaned his team's inability to deal with Stoke's style.
"In the second-half we did better but in the first-half we played exactly the same as we did here last year and probably the same as other teams," Jol said.
"We couldn’t get out of our half, we wanted to try and play football but it was difficult. You get the long balls and they close you down and the pressurise you and when they play their style it is not easy for us.
"We said it before the game that they try to bully teams and they bullied us. It's disappointing because usually we score goals but away from home we couldn't do that today.
"You need self-belief in your quality and don't let them force their style on you and that is what we did first-half, possibly not in the second-half.
"They moan about our style and our fouls, but I know my team and we never foul. I admire Stoke for their style; I always admire teams that have a style.
"It is not my style but it is a style, they are not successful but they do well so we have to stand up and do something against it."