Preheat the oven to 375 degrees F. Lightly grease 14 regular sized muffin tin cups.
In a small skillet, melt the butter over medium-low heat. Add the onions and cook until soft and golden brown, 3 to 4 minutes. Add the corn and a pinch of salt and cook 3 to 4 minutes, stirring occasionally. Remove from the heat and set aside to cool.
In a large bowl, stir together the flour, cornmeal, baking powder, salt, cayenne pepper, and cheese. In a second bowl, whisk together the buttermilk, oil, eggs, jalapenos, and honey. Add the buttermilk mixture to the flour mixture, stirring just until moistened. Stir in the cooled onions and corn.
Spoon the batter into the prepared tins, filling 3/4 of the way full. (If there are empty cups in a tin, fill with water.) Bake the muffins until golden and a toothpick inserted into the center comes out clean, 12 to 15 minutes. Transfer to a wire rack to cool and serve warm.