Rinse the mussels under cold running water while scrubbing with a vegetable brush. Remove "beard" from each mussel. Tap any open mussels gently a few times: if they don't close, discard them. Discard any with broken shells.
Heat oil in a 6 to 8-quart stockpot. Saute the onion, garlic, and thyme for at least 5 minutes. Add the mussels and give them a good toss. Add wine, lemon juice, chicken broth and red pepper flakes; cover the pot and steam over medium-high for 5 minutes until the mussels open.
Toss in the tomato, parsley and butter, recover the pot, and steam for another minute to soften. Serve with rice and grilled garlic bread to sop up the broth.