Preheat oven to 400. Press pie crust into pie plate and crimp the edges. Fill the bottom with pie weights and bake pie shell in preheated oven for 8 minutes.
Heat olive oil in a large skillet over medium heat. Saute onion until translucent and remove. Set aside, leaving pan on heat. Dust tomato slices with flour, then saute 1-minute on each side. Remove from pan and set aside. In a mixing bowl, whisk together eggs and milk and season with salt and pepper. Spread 1 cup of the cheese and basil in the bottom of pie crust. Layer onions over cheese, and top with tomatoes. Pour eggs over the top and spread remaining shredded cheese over the surface.
Bake in preheated oven for 10 minutes. Reduce heat to 350 degrees F and bake for 15 to 20 minutes, or until filling is puffed and golden brown. Serve warm.