The US lost 2-1 to Honduras in their opening game of the final qualifying round in the CONCACAF region and face what Klinsmann has called a "must-win" game against Costa Rica in Denver on Friday before a trip to Mexico next week.
A report in Sporting News cited unnamed players questioning Klinsmann's tactical ability and his approach to the job.
One player said the team was "overtrained and undercoached" while another unidentified player said the German coach was "scatterbrained" in his approach.
But Bocanegra said Klinsmann had always been honest with the players and stressed it was time for the squad to pull together.
"During the last 18 months Juergen has introduced a lot of new ideas to the team and has a vision of how he wants to grow the program," he wrote on his Facebook page.
"Every coach around the world has his own style and methods.
"He has always been up front with players about where they stand and where he sees them going.
"Not every player is going to be happy with all of the decisions and methods, but he will tell you to your face where you stand. From a coach, that is the best thing you could ask for.
"One of the greatest strengths of this team has always been our unity and spirit, and we all remain committed to the cause of qualifying for the World Cup."
Klinsmann left out Bocanegra, the long-standing US captain with 110 appearances for his country, citing his lack of playing time with Spanish second division club Racing Santander.
"Unfortunately sometimes your club situation directly affects your national team career," Bocanegra said in a separate comment on his Twitter account.
The US is fighting for one of three automatic spots in next year's World Cup finals in Brazil through the 'hexagonal' phase of qualifying in a region encompassing Central and North America, and the Caribbean.
Panama and Jamaica are also fighting for World Cup spots in one of the most competitive qualifying phases in the region for many years.
Klinsmann was appointed US coach in July, 2011, and has enjoyed some impressive results in friendly games with first-ever victories in Italy and Mexico, and a 2-2 draw in Russia.
But the team were unimpressive in their initial qualifying phase, losing away to Jamaica and being held to a draw in Guatemala. The Honduras loss has raised the pressure.
"Every home game in the hexagonal is a must-win situation.
You want to get all the points possible in your home games so, independent of the result in Honduras, it's a must-win on Friday night here against Costa Rica," former Germany striker Klinsmann said.
"We approach it that way. I think the game in Honduras was a bit unique. Our preparation was a two-and-a-half day window.
"European (based) players, especially, couldn't adjust to the climate circumstances and throughout the entire team we just played under our usual level."
Klinsmann's plans for the coming week have been hampered by injuries to eight probable squad members and the team is already without all-time leading goalscorer Landon Donovan, who has yet to return from his announced 'break' from the game.