Preheat the oven to 375 degrees. Line a baking sheet with foil or parchment paper and coat it with olive oil cooking spray.
Heat the olive oil in a large skillet over medium heat. Add the ground beef and break the meat into crumbles. Add the onion and the seasonings, then cook for 4-5 minutes, stirring occasionally, until the meat is cooked through and the onion is tender.
Add the minced garlic and cook, stirring constantly, for 1 minute. Remove the beef mixture from the stove and set it aside to cool.
Wrap flour tortillas in wet paper towels and microwave them for 1 minute or until soft.
Place some refried beans down the center of the tortilla, followed by a sprinkling of pepper Jack cheese, then top with some ground beef mixture; roll.
Place the flautas seam side down on a baking sheet. Finish rolling the rest of the flautas, then spray them well with cooking spray.
Place into the oven and bake for 8-10 minutes, then turn over and cook for 5-6 minutes or until crispy and golden brown.
Serve the flautas with guacamole, salsa, and sour cream.