Preheat oven to 350 degrees Fahrenheit.
Using a biscuit cutter or top of a glass, cut tortillas into approximately 4 inch diameter circles. Microwave tortilla rounds on high for 10-15 seconds so that they are warm and pliable. Brush tortillas on both sides with melted butter and press into each cup of a muffin tin so that they form a bowl.
Bake tortilla cups for 10 minutes until slightly golden.
While tortilla cups are baking, sauté onions and jalepeño peppers in a large skillet with the remaining tablespoon of butter over medium-high heat until the onions are soft and translucent.
Add eggs, cajun seasoning and pepper and scramble just until eggs cook through; you don't want to overcook, as they will be going back in the oven. Toss in tomatoes and cheese until the cheese is melted.
Spoon egg mixture into pre-baked tortilla cups and bake for an additional 10 minutes. Garnish with chopped green onion or fresh cilantro and serve immediately.