Heat a large skillet to medium-high; add the brats (casings removed) and cook over medium-high heat until browned and crumbled, using a spatula to break them apart as you go. Remove from heat and drain on paper towels.
Wipe out the skillet, then heat to medium-low. Add the beer and heat until warm. DO NOT BOIL.
Add the cream cheese and cook over medium-low heat, stirring constantly, until the cream cheese is melted and the mixture is smooth.
Stir in the parmesan and shredded cheeses. Continue stirring until the cheeses are fully melted and the mixture is smooth and creamy.
Add the flour, milk and seasonings and stir until incorporated. *If the dip is too thin, slowly stir in additional flour. If the dip is too thick, slowly stir in additional beer.
Remove from heat; add the cooked sausage and garnish with crushed red pepper flakes, fresh chives, and salt and pepper to taste.
Serve immediately with tortilla chips, soft pretzel bites, or fresh veggies. Dip can be kept warm on the stovetop or transferred to a small crock pot on low heat.