Why does so much variation exist within species?
First of all, your assumption is incorrect: those are not genotypes and they do not occupy specific niches. You are talking about phenotypes (eye colour) or in the case of acne, not a trait at all.

I'll answer the question I think you're asking: why does biological variation exist?

Variation is constantly being generated by mutation, errors in the replication of the genome of an individual. If a mutation occurs in the gametic cells, it affects the genotype of the offspring. By affecting the genotype, it may or may not have a discernable effect on the phenotype. Where a gametic mutation isn't fatal, it has a chance of becoming established in the population when that mutant individual breeds. That chance is increased the further along the gradient from harmful to beneficial that effect of that mutation is.

Variation also exists because development responds to environmental factors, not just genetics. Different individuals grow in different environments, and have unique combinations of factors influencing many traits.

The reason variation persists is because, except under conditions of extreme selective pressure or genetic bottlenecks, many traits have no impact on survival or fecundity (reproductive success) or are determined only partly by genetics. Height, for example, only has a very slight impact on fecundity within quite a broad range of heights. It is partly genetically determined, and partly determined by environmental factors such as diet (Eckhardt et al. 2005), exposure to toxins during development, muscular development etc.

If height were the key factor in human mate selection, we might see a gradual reduction in the range of heights, and a gradual increase in average height. However, what we see in reality is that height has changed through human history in concordance with economic factors like social status, inflation and war (e.g. Steckel, 2001), suggesting that nutrition is a major determinant.

I know it wasn't your choice of example, but for more detail on the effects of natural selection on human height, see this question.