The two Bundesliga sides met in Doha with league leaders Bayern sending out an early warning to their rivals in 2013 with Thomas Muller (2), Mario Mandzukic (2) and Mario Gomez on target for the Reds.
"It was too little from us overall," Keller told the Schalke website.
"I would like to see something different from my team in future.
"But I am not going to lose my confidence because of this. The result may have been clear, but we saw some good signs and we also know what is to be improved.
"Furthermore, you've got to recognise our current personnel situation. We had a few players out there who had muscular problems and we had to do without several important players.
"I know what to read into this result and I am nevertheless happy with my team's work so far in the training camp."
Bayern coach Jupp Heynckes was understandably happy with his side's progress at the end of their training camp in Doha, and he knows that his hardest challenge is to keep his players' feet on the ground.
"We will not veer off route," he said. "Nobody is going to get carried away.
"I know that this is only a step of our preparations. I told the players this morning that we must carry on the way we are going."
Bayern return to Bundesliga action on January 19 with a home game against bottom-placed Greuther Furth.
They carry a nine-point lead into the second half of the season with Schalke a further eight points adrift in seventh place, although he [Keller] knows he has a lot of work to do before the Bundesliga restart in 10 days' time.