Why Decision trees performs better than logistic regression
Have you considered using a neural network for this? The challenge with the two approaches you're using is that both models are not great at handling a large number of features and you, essentially, have 10,000 features. So, my guess is that even with the decision tree,  you're probably just picking up some background pixels that are inflating your accuracy rate. There's probably something there that the decision tree is picking up and then "locking" you into that branch of the model, which is less than ideal. Using a neural network can help you create a model that can do more nuanced choices