There were not any political differences between Afonso and his mother in the way we think of political differences today. It is not as if Afonso was a liberal and his mother a conservative or anything like that. These were the Middle Ages and "political differences" were typically just differences over who should have power over what. Basically, the difference between Afonso and his mother is that he wanted to rule Portugal and so did she.
Basically, many of the barons (the lesser nobles) of Portugal felt that their fortunes were declining. The county (an area ruled by a count) of Portugal was constantly being invaded by armies from other parts of the Iberian Peninsula. (Remember that there was no Spain at this point and that there were, instead, all these small political entities like Leon and Galicia and Portugal.) The nobles in Portugal felt that this was the fault of Teresa and the lover that she had taken when her husband died.
The nobles, then, started to look for someone else to be their leader. Afonso was convenient because he had the right bloodlines. In addition, Afonso had taken the side of the Archbishop of Braga in his struggle against a fellow bishop that Teresa backed. The nobles turned to Afonso as their leader and he led them against his mother.
So, the differences between these two were mainly based on their (and other people's) desire for power and control, not on any ideological differences.