Heat a small skillet over medium-low heat and melt the butter. Add the red onion and jalapeño and saute for a few minutes. Add garlic and saute for one minute. Add chipotle pepper, chili powder, salt, and pepper.
Add the flour and stir constantly for 1 minute.
Pour in ¼ cup of the milk, then the cream cheese. Stir constantly and cook until thickened and smooth, about 2 minutes.
Slowly stir in the remaining ¼ cup of milk and cook until combined and starting to steam. Add the shredded cheese. Stir constantly until the cheese is melted.
Stir in cilantro and serve immediately with tortilla chips