Judge Hudson's decision concerning the Commerce Clause ultimately rests on three related analytic moves, which together render the minimum coverage provision beyond the commerce power.
1. ACA 1501(b) regulates "inactivity" -- the non-purchasing of health insurance. This rejects the United States's conception of the regulated activity as a conscious decision of how to finance health care. From the United States's perspective, everyone is engaged in the health care market. 1501(b) therefore regulates a choice as to the financing of that activity, making it a regulation of affirmative action (and an economic one at that).
2. The commerce power, categorically, does not reach inactivity. Unless the regulated individual has made some "self-initiated action" to enter the relevant market (here, the health insurance market), Congress cannot regulate that individual pursuant to its commerce power.
3. The Necessary and Proper Clause affords Congress no additional leeway in that respect. That is, just as Congress cannot regulate this "inactivity" directly under its commerce power, nor can it regulate such activity as an "appropriate" means to effectuating a broader regulation of a commercial market.
There are a few additional details, but those three points constitute the essence of Judge Hudson's decision.