Yeah, stinky's right about the heterozygous traits. Most living things have two sets of DNA, one from the mom and one from the dad. These sets will always be mostly the same, but occasionally, you'll have two different genes, or alleles. Often, the genes are dominant or recessive, meaning only one type will express itself. But sometimes, genes can be codominant or incomplete dominant, meaning both sets of DNA express themselves. When you cross a plant with itself, only half of the heterozygous traits (ie, traits where the two alleles are different) remain the same with the offspring.

A lot of the really awesome plants are hybrids, meaning the two parents are quite different. This means that a lot of the offsprings' genes are heterozygous, so pollinating one of these hybrids with itself will get rid of a lot of the heterozygous traits, and having some of these heterozygous traits may be what makes the plant so awesome.

In most cases forcing a hermie will not make the offspring more likely to hermie, especially if you're pollinating within an inbred line. If there is a gene that increases susceptibility to hermaphrodite phenotypes in your gene pool, then you may be bringing it to the forefront, but most good lines have probably had the hermie genes bred out of them by now. Anyway, the problem usually isn't due to breeders that breed for themselves, it's due to seed banks that sell feminized seeds from plants that hermie really easily. Which means those plants may also hermie easily for you, which is probably a bad thing.