Heat olive oil in a large skillet over medium-high heat. Add onion and red pepper flakes, and cook stirring constantly until onion is tender. Add garlic, and cook for a couple of minutes, just until fragrant. Pour in the reserved clam juice, and simmer over low heat for 10 minutes.
Bring a large pot of lightly salted water to a boil. Add linguine pasta, and cook for 8 to 10 minutes, until al dente.
Add clams to the sauce, and cook just until clams are heated through, or they will become tough and chewy. Remove from heat, and serve over linguine pasta. Top with a sprinkle of grated Parmesan cheese.
