See this very important interview that FEC Commissoner Brad Smith gave to the A.P. Here’s a snippet of why Smith thinks that the FEC may have to treat the 527s as political committes subject to FEC regulation:

Smith said that while he hasn’t formally made up his mind, he believes the court’s ruling may require the FEC to treat the new groups just like regulated political committees. As such, they would be limited to accepting no more than $5,000 in donations from each individual, and be banned from taking corporate or union money.
It also would require them to disclose their finances and spending to the FEC.
Smith said the high court ruling seems to eliminate the court’s previous “express advocacy” standard, which meant the FEC could regulate groups that spent money expressly calling for a candidate’s election or defeat.