Heat the oil in a large saute pan with a tight-fitting lid over medium-low heat. Add the garlic, salt, pepper and red pepper flakes and saute until fragrant; don't let the garlic brown. Add the cherry tomatoes, white wine and clams, increase the heat to high and cover the pan. Cook, stirring occasionally, until all the clams have opened, about 8 minutes. As the clams open, transfer them to a large bowl. When all the clams are removed, reduce the heat to medium-low and swirl in the butter. Season with salt and pepper.
Meanwhile, bring a pot of generously salted water to a boil. Cook the linguine according to the package direction. Using tongs, transfer the linguine to the saute pan with the clam juice and toss to coat. Turn off the heat and add the clams and any juices that have collected in the bowl, the lemon zest and half of the basil. Using tongs, turn the linguine to coat it with the sauce. Top with the remaining basil. Serve immediately.