He said: "We were not lucky. It was a very close match and I think we had more clear options than Blackburn but we played against a very strong team who were at home.
"They had a lot of motivation and that is normal when you have a Championship team playing against a Premier League team.
"I'm not disappointed. Of course, everyone wants to win all of the games but we were playing against a very strong team at home.
"I am sure if they played like that in the Championship they would be in another position in the table.
"I would be disappointed if we lost and were out of the FA Cup but we are not out and we must play at home."
There were claims that Pellegrini intended to take off Edin Dzeko with the score 1-1 in the second half but the wrong player's number was held up and Negredo was substituted instead.
Asked if a mistake occurred, Pellegrini said: "No."
Pellegrini was not critical of goalkeeper Pantilimon, who returned to the side for the tie after recently losing his place to Joe Hart.
The Chilean said: "I will analyse the game with the players, as a collective team.
"Maybe (he dropped the ball) but always the individual performance makes the team performance, so I analyse what the individual players do with them."
Pellegrini added he had "no complaints" about Boyata's dismissal for a second bookable offence.
A number of Rovers players impressed, not least Cairney and Rudy Gestede, just a day after making their loans from Hull and Cardiff respectively permanent.
Former England goalkeeper Paul Robinson, playing his first game in 13 months and now fully recovered after a blood clot on his lung, also made some crucial saves.