Here's a snippet from the ACLU site.
Public health authorities make mistakes, and politicians abuse their powers; there is a history of discriminatory use of the quarantine power against particular groups of people based on race and national origin, for example. The lack of checks and balances could have serious consequences for individuals' freedom, privacy, and equality. The Act lets a governor declare a state of emergency unilaterally and without judicial oversight, fails to provide modern due process procedures for quarantine and other emergency powers, it lacks adequate compensation for seizure of assets, and contains no checks on the power to order forced treatment and vaccination.
It goes well beyond bioterrorism. The act includes an overbroad definition of "public health emergency" that sweeps in HIV, AIDS, and other diseases that clearly do not justify quarantine, forced treatment, or any of the other broad emergency authorities that would be granted under the Act.
It lacks privacy protections. The Act requires the disclosure of massive amounts of personally identifiable health information to public health authorities, without requiring basic privacy protections and fair information practices that could easily be added to the bill without detracting from its effectiveness in quelling an outbreak. And the Model Act would undercut existing protections for sensitive medical information. That not only threatens to violate individuals' medical privacy but undermines public trust in government activities.
The act is a throwback to a time before the legal system recognized basic protections for fairness; before public health strategies were rooted in voluntary compliance; and before the information age dictated the need for privacy protections of individuals' personal information.