The Portuguese coach made nine changes for the fifth-round tie at Craven Cottage, yet watched his side slump to a painful 1-0 loss after a dramatic late penalty from Ross Stewart.
Fulham dominated possession and fired 24 shots but struggled badly with their finishing. Despite controlling large periods of the match, they failed to seriously test goalkeeper Daniel Peretz and paid the price for their wastefulness.
Silva named several experienced players in his rotated side. Samuel Chukwueze, Oscar Bobb, Rodrigo Muniz and Ryan Sessegnon all started, while veteran midfielder Tom Cairney added leadership. Key attacker Harry Wilson missed out through injury.
Speaking after the match, Silva made it clear he believed the issues ran deeper than rotation.
"It's more than that," Silva said. "It was a bad afternoon for us and for our fans. We need to look deeper because I'm not pleased at all with what happened.
"If it's because of the changes then fine, I understand that. But Sessegnon and Timothy Castagne have played this season against top Premier League sides, while Oscar Bobb and Samuel Chukwueze are at the level."
Silva accepted responsibility but defended the strength of his squad.
"I understand I get the blame for making the changes," he said. "Nine changes are nine changes, but I see it differently because these players have started many games for us this season."
The Fulham manager pointed to poor efficiency in the final third as the decisive factor.
"When you have 24 shots and they don't create many clear chances, it's simple," he explained. "We reached their box often and created from wide areas, but the end product was not good enough. We have to finish better, be quicker and arrive in the right positions.
"They had five shots and were dangerous on the counter. It's about mindset. Our end product was not at the level it should be."
Fulham supporters voiced their frustration at full-time, but Silva promised a strong response as the club turned focus back to the Premier League campaign.
"It's our obligation," he said. "We must accept it was a very poor afternoon. Anything can happen in football, but this was more than that.
"We have to look deeper, and that starts with me."
Pep Guardiola has insisted mentality and personality would define Manchester City's season run-in after his side powered into the FA Cup quarter-finals with an impressive 3-1 win over Newcastle United.
FC Barcelona midfielder Fermin Lopez has said the squad were in "good spirits" after their important La Liga victory and warned they must be ready for a demanding physical test against Newcastle United in the UEFA Champions League on Tuesday.
Mikel Arteta heaped praise on 16-year-olds Max Dowman and Marli Salmon after they helped Arsenal reach the FA Cup quarterfinals, describing their performances as “exceptional” and a sign of the pair's quality and personality.
Chelsea head coach Liam Rosenior defended his decision to heavily rotate his squad after his side needed extra time to beat Wrexham 4-2 and reach the FA Cup quarter-finals.
