The Belgian international has made only two appearances for the Gunners this season following his return to full fitness after a back problem, with Per Mertesacker and Laurent Koscielny striking up a good understanding at the heart of the defence.
Vermaelen, who joined Arsenal in July 2009 from Ajax and succeeded Robin van Persie as skipper last season, remains relaxed about the situation, but accepts it is far from "ideal" not to be playing regular football ahead of the 2014 World Cup.
While Wenger can see the contradiction in a captain being kept sidelined, the Arsenal boss maintains the collective good must continue to outweigh any individual needs.
"It is not down to logic, but it is part of the decision you play the best pair and I must say the pair worked until now, so it is difficult to change," Wenger said.
"I named him captain but usually you name as captain a player you rate and a player with good behaviour as well.
"Vermaelen is a top guy with fantastic attitude.
"I don't worry for him because he is a very strong guy.
"At the moment he doesn't play, although that can change quickly.
"Sometimes players who don't play in September or October, by March they are the main players. The important thing in our job is never to give up. You have to stay and fight."
Wenger, though, stressed: "We are in a job where you have to be ready when you are needed, that is the job of the players to continue to compete and you have to accept the competition.
"The big players want to be with big players, but the disadvantage of being with big players is that you are not that sure to play.
"Unfortunately when you have 20 good players, nine good players don't play.
"You cannot have everything."
When all of his squad are match fit, Wenger certainly will have something of a selection dilemma - with the likes of England forward Theo Walcott, France Under-21 international Yaya Sanogo, German forward Lukas Podolski and England midfielder Alex Oxlade-Chamberlain all hopeful of featuring again over the next two months.
The recovery of Abou Diaby, however, remains slow, with the combative Frenchman needing further minor surgery to aid rehabilitation following knee ligament damage which has again hampered his progress this season.
"He had a little key hole surgery again on the knee because his knee blew up every time he did something, so it is now six months after the cruciate," Wenger said.
"He could not even jog yet. With new surgery it is a setback for him, so competitive football cannot be played before March."