Beneath the politics of convenience is the reality that a large segment of the U.S. government really does operate without much transparency or public scrutiny, and has abused its awesome powers in myriad ways. And sometimes the government bureaucracy really does exercise power over the commander in chief...
Whether any of this means there is a deep state in America depends on your definition. Powerful bureaucrats with access to government secrets and trusted media friends certainly do try to influence presidents from the shadows. But in Washington, at least, their views and goals are not monolithic.