Do we negatively perceive people who wear glasses? If so, why? Is it cultural stereotypes, a simple case of homophily, or is there more to it?
No, people wearing glasses are not generally perceived negatively. Glasses affect various dimensions of person perception differently. To name a few, a commonly reported effect you may want to read up on is the glasses stereotype: If you wear glasses, people will tend to think of you as smarter (e.g., Hellström & Tekle, 1994, Terry & Krantz, 1993), but less attractive compared to those not wearing glasses (Hasart & Hutchinson, 1993; Lundberg & Sheehan, 1994; Terry & Kroger, 1976). This effect has been found regardless of whether the judges wear glasses themselves, although, when they do, the effect on attractiveness appears to be less pronounced (Terry & Kroger, 1976).
It appears, this effect is also moderated by the type of glasses you wear:
(From this online summary of Leder, Forster & Gerger, 2011)
The simple answer is that it depends on the person.
Whenever you're talking about a perception, you have to first realize that perceptions are built on many things. Since a person's upbringing, social group, age, IQ, beliefs, expectations, and past experiences (to name a few) can affect one's perceptions, there is rarely a simple answer as to if, or why someone would have a particular perception.
That said, here's a few things that could have an effect on someone's perception.
People could very well have positive perceptions of people that wear glasses. There can be the perception that people with glasses are smarter/more intelligent and if the perceiver also wears glasses, it would be something they have in common, thus making them perceive them in a more positive light.
On the negative side, there could be the perception that those with glasses are weaker, old, more fragile or genetically inferior than they are. However, from my experience, generally the only people that have a negative percept of those that wear glasses are children and teens who are simply trying to find something different about another person in order to tease them, (or worse) not because of any thought out reason.
This would probably line up with parts of homophile, but not in the truest sense of the word as it would depend on the person.
As far as cultural stereotypes, they can surely affect one's perceptions of a people group. however, these stereotypes can be both good and bad.