Star Trek: Voyager's Robert Beltran was introduced as a Maquis leader who had been misled by Tuvok [Tim Russ]. Of course, he didn't find out about that until he was aboard Voyager. Fans wondered how he was so easily fooled, and that wonder escalated when we discovered he'd been duped by Seska [Martha Hackett] as well. How could someone who was supposed to be in command be so easily manipulated?
Sometimes, when rewatching Voyager, we can still find ourselves asking the same question, mainly because we're on the outside looking in. We think it's something we ourselves would have seen. But Beltran himself doesn't see it that way. Beltran was interviewed in Star Trek: Voyager magazine during the series' second season, and he wasn't concerned about Chakotay being deceived as he called Tuvok and Seska "formidable, intelligent, and subtle people who could fool most anyone and get away with it."
While we saw something we didn't like with Seska and questioned her from the beginning, it would not have been as easy to see that with Tuvok, who, being a Vulcan, is a master at controlling his emotions. Even a Romulan commander was fooled by Spock [Leonard Nimoy] when Romulans are a cunning, powerful people. And for Seska, Beltran called her "quite a mental chess player and manipulator." She also fooled B'Elanna Torres [Roxann Dawson] as well.
Beltran went on to say that "with Chakotay, once you have his loyalty, he doesn't bat an eye and question something unless it's glaringly obvious. He's willing to give everybody the benefit of the doubt if he feels loyal towards them and believes they're loyal towards him."
In short, Chakotay trusted the people he worked with. He thought they were his friends as well. While he was fooled, it didn't make him less of a leader. He led with his heart sometimes, and after being in a relationship with Seska, it would be hard for him to imagine her betraying him. But Chakotay, like the rest of Voyager's crew, learned from his mistake, and he wasn't so easily fooled after that.