Position racks in the upper and lower thirds of the oven; preheat to 425 degrees F. Toss the onion and peppers with 1 tablespoon olive oil on a baking sheet. Season with salt and 1/4 teaspoon red pepper flakes. Bake on the lower oven rack, turning once, until slightly golden, 15 minutes.
Meanwhile, line another baking sheet with parchment paper. Combine 1 tablespoon olive oil, the fennel seeds, remaining 1/4 teaspoon red pepper flakes and a pinch of salt in a small bowl. Brush the tofu pieces on both sides with the oil mixture and transfer to the prepared baking sheet. Bake on the upper oven rack until golden, 15 minutes.
Brush the roll bottoms with the marinara sauce. Top each with 2 slices tofu, some onion and peppers and the roll tops.
Whisk the remaining 1 tablespoon olive oil and the balsamic vinegar in a medium bowl; season with salt and pepper. Add the arugula and toss; top with the parmesan. Serve with the subs.