I think you got confused with the notation you saw in the output on your last slide. %-1, %-2 etc. is not the charge of the microspecies, it is simply the number of the microspecies, so 1st, 2nd etc.
So in the case of the ammonia, the 2nd (green) microspecies is the major form (ammonium cation), as the pH is acidic. Therefore you will find the molecule mostly in a protonated state, with +1 charge.
If you set your pH range to (8,9) for example, the ratio of the ammonia present in the solution will be higher.
I hope this helps,