An augmented chord has nothing to do with a minor chord. Yes, there is a major 3rd between the 3rd and 5th, but in the augmented chord that interval is being built off a major 3rd, not a minor 3rd like in the minor chord.

Aminor: A(R), C(3rd), E(5th)
A aug.: A(R), C#(3rd), E#/F (5th)

Try note to relate the sound qualities to each other, but to see (hear) them for what they are. A minor chord is not a major sound w/a flatted 3rd...this is not a good way to look at things. For instance, lets take colors for example, not many people look at Orange and see yellow and red, they take it for what it is, orange. Each sound quality is its own entity: Major, Minor, Dominant, Augmented, Diminished.