In a large pot over medium high heat, melt butter. Add in onions, carrots and broccoli. Cook to soften about 5 minutes (may be more or less depending on the size vegetables you cut).
Slowly add in broth and milk. Sprinkle with flour and add salt, pepper and red pepper flakes. Continue stirring and heating over medium heat until thickened. This will take about 10-15 minutes.
Once thick, add cheese and stir until melted and smooth. Serve soup and enjoy!