The last generation of control freaks had figured out how to use religion as a medium for their desires. They were caught flat-footed by new internet media like everyone else.
The next generation have now learned how to use twitter. The basic tactics probably haven't changed that much but the details of the message are new. I doubt education was a driving issue as this is more an issue of personality types.
Secularism vs religion is a red herring. Society became freer because people began to value (classically) liberal ideals--i.e., people came to value freedom as a principle. Liberalism is secular but secularism isn't liberal (nor is it inherently illiberal), and there have been many illiberal secular ideologies not only in theory, but in practice (e.g., practical communism of the 20th century wherein people were literally executed, imprisoned, exiled, etc for their free speech). And of course what we see today.
Secularism isn't a virtue, liberalism is.