Preheat oven to 400 degrees F (200 degrees C). Bake pie shell in preheated oven for 8 minutes.
Meanwhile, heat olive oil in a large skillet over medium heat. Saute onion, garlic & red pepper until soft; remove from skillet. Sprinkle tomato slices with flour and basil (or if using fresh basil add as layer in step 2 on top of onion mixture, then saute 1 minute on each side. In a small bowl, whisk together eggs and milk. season with salt and pepper.
Spread 1 cup shredded cheese in the bottom of pie crust. Layer onion mixture over cheese, and top with tomatoes. Cover with egg mixture. sprinkle top with remaining 1/2 cup shredded cheese.
Bake in preheated oven for 10 minutes. Reduce heat to 350 degrees F (175 degrees C), and bake for 20+ minutes, or until filling is puffed and golden brown. Serve warm.