After battling through to secure a podium in the first race of his Yamaha return, Rossi headed to Texas aware that Honda could dominate given its pre-season form at the circuit.
As a consequence Rossi said he started the race on the defensive and with a top-five finish his main target.
While Lorenzo and Cal Crutchlow on the satellite Tech 3 Yamaha were able to achieve that, Rossi felt a brake issue meant sixth was the best he could manage.
"This is a difficult track for us," he acknowledged.
"We expected to do better, but I had a lot of problems in the race because I had a problem with the brakes.
"I had a vibration in braking because I lost one part of a disc so this didn't help.
"We knew that we had to defend here; we know that when we cannot attack we need to try and arrive in the top five but today it was sixth.
"The balance of the first two races is positive and we arrive in Jerez optimistic for the next few races as the tracks are better for us."
Yamaha team boss Massimo Meregalli said pre-race set-up tweaks had also proved ineffective for Rossi, although he insisted he was happy with the team's return of third and sixth from the race.
"Vale's team worked really hard to try and fit the bike to his riding style; they improved the bike through each practice," Meregalli said.
"Unfortunately we made another step from the warm up to the race that didn't work as we expected. He also had a vibration on the front from his brakes.
"I think we are leaving Austin in a really good shape and we are really looking forward to the Jerez race."