The Hornets lost 2-1 to Crystal Palace at Wembley to end their impressive cup run at the penultimate stage but Flores was quick to turn the defeat into a positive as the Hertfordshire outfit look to achieve the major objective they set out to achieve at the beginning of the season.
"The players feel positive," said the Spaniard.
"Everyone is disappointed but we need to be realistic. No one expected us to be in the semi-final.
"When we started the season the main target was to stay in the Premier League. That's the most important thing for Watford.
"We need reasons to be happy, to be positive. I don't see why we have to be negative.
"We were competitive and created chances. But we did not expect to concede with the first play.
"But Crystal Palace have a great team and a great manager, and congratulations to them."
However, Connor Wickham spoiled the party for Watford when he nodded Pape Souare's cross beyond Costel Pantilimon in the 61st minute to set up the decider with Manchester United at Wembley next month.