Marko, a motorsport advisor for Red Bull, told the company's own in-house magazine earlier this month that he felt Webber lacked the consistency and psychological strength to win a world championship.
At the launch of the Red Bull RB9, Horner distanced himself from Marko's opinions.
"We all know Helmut can be outspoken at times. His comments reflected his opinion, and these things can be misinterpreted," Horner said.
"If we weren't happy with Mark we would never have signed him for this year.
"We give both drivers equal opportunity and it's down to what they do on the circuit.
"Certainly in the team, that's the approach and we'll continue to do that.
"For us, it doesn't matter which driver wins as long as it's in one of these cars."
Webber added that he did not let Marko's comments have any effect on his self-belief, and that he would not be at Red Bull if he doubted the team had faith in him.
"I do believe I can have a crack at the championship again this year, as I have done in previous seasons," he said.
"That's what I'm getting up each day thinking.
"The team know I need 100 per cent support. You cannot win world championships with 90 per cent support.
"That's what I'm confident of."