Are you punished from Hashem if you don't do a mitzvah asey (brachos, davening, asher yatzar, etc.)?
Generally, no (with a couple of exceptions - failure to bring the Korban Pesach, or to undergo a bris milah - both of which are punishable by kareis).
However, the Gemara (Berachos 26a, Chagigah 9a-b) classifies failure to perform other positive mitzvos as מעוות לא יוכל לתקון - a crooked thing that cannot be straightened out. Or in the formulation of Tanya (Iggeres Hateshuvah, ch. 1), האור נעדר - the Divine "light," that should have been drawn down by the mitzvah-action, is missing.
There are different types of positive commandment with respect to punishment.
One type is obligatory on the person, such as wearing tefillin or saying shma.
Another type isn't an obligation upon the person, such as tzitzis, which is only obligatory if one wears a four-cornered garment, or mezuza, which is only obligatory on residents of a home. One can go his whole life without such a garment or home and never be obligated to do the mitzvah.
The Talmud in Menachos (41a) states that, for the latter type of mitzva, during times of Divine anger, one is punished for not having obligated oneself and performed the mitzva. Clearly, the first type of mitzva incurs penalty all the time.