Correct, an axiom is an assumption. Logic starts with assumptions, then you make deductions from them. This does not make math illogical any more than it does any other logic that starts with an assumption.
http://en.wikipedia.org/wiki/Axiom
Take Special Relativity, for example. Evidence suggests very strongly that the speed of light is constant, but since all knowledge is tentative due to the inability to test absolutely every case, it has to be considered an assumption as a basis for starting a mathematical/logical analysis of the issue.
As suggested above, you appear to be making the mistake of believing that what is counter-intuitive is illogical. That's wrong. Humans perceive the world mostly on Newtonian time and distance scales and prior to 1900 assumed that the universe worked in a Newtonian way on all scales. It is not an unreasonable assumption, but it happens to be wrong. But since we go through life perceiving the world in that way, it is difficult to accept that it is wrong. That's why we consider Relativity and QM counter-intuitive when we are first exposed to them, even though logic shows us that they are more correct than the Newtonian view.
Starting with the assumption that the universe is Newtonian because we don't know any better is a fine assumption, but hanging on to that assumption when it is proven to be wrong because experience makes it intuitive is most decidedly illogical.
Going back to the OP: That isn't illogical. Light displays traits of both waves and particles and therefore is modeled that way. That's completely logical! Similarly, water displays both bulk fluid properties and discrete particle properties. It can be modeled as either depending on what you are trying to investigate.