Leonard Boyle, the head of the FBI's Terrorist Screening Center, said on C-Span that some 200,000 individuals are considered to have 'some relationship with terrorist activities,' a designation strong enough to keep them from boarding airplanes.
Their names are contained in the FBI's watch list, which apparently totals 400,000 names (not the million cited in news stories - the higher number apparently includes variations in spelling). Of those, some 5-6% are U.S. citizens or legal residents. Read more in this editorial in Investor's Business Daily. And, if you want another opinion about the list, there's a GAO report from last October assessing that it has helped U.S. agencies to combat terrorism.
The FBI's assessment is consistent with the findings of a Pew survey of American Muslims released about a year ago. The survey found that 15% of American Muslims under 30 said suicide bombing was often or sometimes justified, You won't find that statistic in the summary, but it's on page 53 of the full report. Incidently, the survey also found that 60% of Muslim Americans did not believe that Arabs carried out the 9/11 attacks. So if you're feeling complacent about America's security relative to that of Europe, you might want to rethink.