For the same reason Monsanto sequences basically anything: Because we can tell what proteins are encoded in there, and what is near them, and we can have good ideas of what proteins are expressed together. When dealing with genetic modification, we get to see whether our modification went in, and where it landed: Having a protein in a genome isn't enough. Its expression might be having an effect on other things, depending on where it is.

When we have baselines, we can compare different individuals, and eventually make predictions of how they are going to be based solely on the genetic code. If I know that a certain polymorphism is tied to some trait I want, I might not have to even bother spending the time growing a plant: I know that it's not what I want, and discard it as a seed.

With humans we are probably not going to see much modification soon, but just being able to detect genetic diseases, risk factors for other diseases that have genetic omponents, or allow for selection of embryos in cases of artificial insemination is already quite valuable.

It's not source code that we are all that good at understanding just yet, but there's already some applications, and we have good reason to think there's a lot more to come