It is probably rusted to the spacer tube inside the wheel. It is a bugger to get any penetrating fluid into, as you will have difficulty getting in past the oil seals. Try laying the bike on its side and put wooden blocks under the swingarm either side of the axle, this way you can start to drift it out without the swingarm 'flexing' and taking the power out of the blows. This method is coarse though, and is likely to leave you needing to replace the axle as the threads will be nadgered. You can try to protect them by putting the nut on, but tricky to avoid damage....at least you should be able to get it out though.