If strings of matter are of the same substance how can matter carry differing charges? Considering that a string is a loop of energy composed of the same underlying material how is it possible for it to be either positively or negatively charged? For that matter, how is it possible for it to be the same substance and to have zero charge?
 A: The standard model of particle physics has these basic elementary particles

There is an equivalent table of antiparticles . Note that they come with charge mass and spin assigned. It is an experimental fact that has to be fitted in any mathematical models.
String theory models that want to describe elementary particle physics, must be able to embed this structure and the $\operatorname{SU}(3) \times \operatorname{SU}(2) \times \operatorname{U}(1)$ group structure which these particles obey. ( also any theory that aims at becoming a theory of everything).
The string is a generic string, and its excitations are the ones that have to map onto the particle table, and obey the group structure above.
So a specific particle is a specific excitation of the generic string, and the excitation level carries enough quantum numbers to accommodate all particles in the table, charges and spins and all.
In the standard model, each particle is represented by a point. The point may be considered generic on which the particles are labeled. When the standard model is embedded into a string model, the point becomes a string, that's all.
Edit after comment:
The misunderstanding comes here:

Considering that a string is a loop of energy 

It is not a loop of energy, a string is a mathematical locus of one dimension, of the same type that a point, in the standard model representation of particles, is a locus of zero dimensions.Both are used as representations of particles with a lot of quantum numbers and carrying a four vector describing the particles, with momentum , energy and invariant mass. These are assignments on geometrical loci. The point loci of the standard model have to be assigned on one to one representation to the group structure of the standard model, $\operatorname{SU}(3) \times \operatorname{SU}(2) \times \operatorname{U}(1)$ . String theories allow a structure on the vibrations which can accommodate the standard model group structure and thus are a candidate for a theory of everything, as they also allow for the existence of gravitons on their own vibrational level. That is the progress in theory.
