One of my conspiracy theory-loving friends posted about this patent, thinking the government created ebola for the purposes of population control. This is obviously hogwash, but I don't quite get the dense language - what is the point of this patent?
Having skimmed though the patent, it looks like it is a patent for a weakened version of the virus, that is taking the existing virus and making it non-threatening -- it is certainly not a patent which is supposedly creating the virus.
Weakened version of a virus and disease agents in general are desirable for research purposes, so that they can be studied in laboratories without any unnecessary risk to staff or for using it in a vacination effort.
The process of weakening the virus is known as 'inactivation' and you can read more about it on wikipedia here.
Your yearly flu short contains flu virus which has been 'inactivated' and you can read more about it here
Exact purpose for the patent is very likely basic research which is why it is being done by the government rather than by some private institution. As the motivation, it is very likely to gain sufficient information of the virus to defend against it should it ever come to the US as an outbreak.