Preheat oven to 350 degrees. Line a rimmed baking sheet with aluminum foil.
Chop tomatoes into approximately 1 to 1½ inch pieces. Spread out evenly on baking sheet along with onion, garlic, and thyme.
Bake for 1 hour. Increase oven temperature to 400 degrees.
Whisk together honey, oil, vinegar, salt, black pepper, and red pepper flakes in a small bowl. Drizzle over tomatoes.
Return pan to oven and bake for 45 minutes, stirring every 15 minutes. Let cool. Scrape all contents of baking sheet into a bowl. Stir to combine, mashing while you stir to break down the tomatoes and form more of a cohesive mixture.
In a food processor, process cream cheese and feta until smooth. Add olive oil and process until mixed.
Spread each baguette slice with whipped feta and top with tomato jam. Garnish with thyme if desired.