Because the military isn't supposed to act domestically under normal circumstances, to prevent other kinds of abuses. So we have a federal police organization

Because the military isn't supposed to act domestically under normal circumstances, to prevent other kinds of abuses. So we have a federal police organization separate from the military, theoretically trained to obey the rules of domestic operations (eg, constitutional protections). And it is that police organization which handles intelligence about, eg, terrorism and foreign spies that originates inside of the country. There are some caveats about cooperation between different agencies, but I'm not going to try and defend those as they currently exist -- the domestic police shouldn't have access to some of our spy apparatus that doesn't obey domestic laws. However, there is a legitimate reason to have a domestic police force separate from the military, and a legitimate need for them to have some intelligence operations, to eg crack terrorist rings and track spies.