I think that something that gets kind of ignored rather often is how Thomas earned Minho's loyalty by being everything he could not be.
Even though Thomas is not the prettiest٫ nor the most physically fit Glader٫ it was his bravery and courage when entering the Maze and insisting on saving Alby that made Minho follow him to the ends of the earth.
Minho didn't just see freedom in Thomas٫ he also saw a much better person than he was٫ and someone he wanted to be like٫ making that seemingly crazed Greenie deserving of his unquestionable loyalty.
For Minho٫ Thomas was hope in freedom٫ but also hope in a better future where he could overcome his fears and get rid of everything that held him down٫ including himself.
Minho valued freedom above anything else٫ and to him٫ Thomas embodied both freedom from his physical captors٫ and from the self imposed jail he'd been living in until then٫ pretending to be someone he was not and letting himself cower when faced with true fear. Thomas changed that when he faced down against a Griever٫ and forced Minho to face his real self. forcing him to accept he was a coward٫ and then change himself for the better٫ turning into the brave (if flawed) leader he later became.