They’re not.
Minecraft bees are just bees. Yellow, black, fuzzy, occasionally aggressive if you mess with their nest. Mojang has never said they’re trans, the code doesn’t flag them as trans, and there’s no lore entry that reads “this bee identifies as.”
Someone online almost certainly made the claim as a joke, a troll, or a extremely online attempt to start a fight. That’s usually how these “why is X trans?” questions start. The bee itself remains ideologically uncommitted and mostly interested in flowers.