Hugo Duro fired Valencia ahead before Ayoze Perez found Villarreal's equaliser. Pape Gueye was sent off for the visitors on 68 minutes.
Baraja said: "It is a bittersweet feeling. I think we did enough to win the game. We leave here with only one point. It is a little reward for what we saw in the game. Football is like that. We are in that moment in which the opponents when offering little, can complicate the game for you.
"We have to take away the fact that the team's work has been good and continuous. There is an improvement -not in the result, but in what we want to be and where we want to go.
"This assessment cannot be made until time has passed and we show what the team's performance level is. The young squad we have gives us the possibility of having competition for positions that we did not have last season. Now, we have to get the most out of it. Last season is over. New players have just arrived and we will have time to work. The objective is set on the pitch and game-by-game. The club will come out to assess what the objective for the season is."
He also said: "An aspect to improve is the management of the closing minutes. We have to know how to manage these types of moments to go into halftime 1-0 up. We were unlucky in that action. It was Vilarreal's first shot.
"It is cruel to go into halftime with that scoreline, but we have to pick ourselves up like we did in the second half. We did everything possible to win, but we did not have the luck we have had on other days.
"The team were energetic and believed in what we were doing. We had opponents in a good dynamic in front of us, and today they felt uncomfortable and did not create many difficult situations for us."