Muffins may make a tasty treat for breakfast, but they are not Paleo-friendly. Anything that is made with wheat flour (or any grains, for that matter) is off the Paleo menu.
Wheat As a Nutrient-Deficient Food
Flour is highly refined. The amount of effort required to turn grains into edible flour is not worth the minimal nutrition the seeds contain and our cavemen ancestors wouldn’t have bothered. In trying to eat a diet closer to that which our paleolithic ancestors consumed, we have to consider what they ate and why. In general, they went for the most nutritious food, which meant going straight for organ meats whenever there was a kill, and eating lots of fruits and vegetables. Grains are very low in nutrition and high in carbohydrates. Their prevalence in the Standard American Diet (SAD) is largely responsible for our declining health.
Paleo and Sugar
In addition to the flour base, muffins also tend to contain added sugar, which exacerbates the negative effects of the flour. Although sugar eaten occasionally can be relatively harmless, eating it on a regular basis (especially with other foods that have a high-glycemic load, such as flour) can lead to inflammation and insulin resistance. Insulin resistance is a metabolic disorder that is a precursor to everything from diabetes to cancer. Inflammation also plays a role in these diseases, and inflammation (not cholesterol) is the real culprit behind heart disease.
For more reasons to avoid gluten, check out this post by Grassfed Girl.