One of the major things that has stopped the free flow of ideas at times in our history is the fact that people have thought that various kinds of ideas were bad. This has been seen at many points in our history.
For example, during the McCarthy Era, the free flow of ideas was threatened. This was because people were afraid to talk in any sort of positive way about communism or even to defend the right of others to be communist.
In modern times, "political correctness" endangers the flow of ideas. For example, when the president of Harvard University tried to discuss his ideas about why there were fewer women in sciences and engineering and such, his ideas were shouted down by people who thought that they were sexist -- they were criticized not on their merits, but on the fact that they were seen as offensive.
there are many things that have threatened the free flow of ideas in history, Since history is nothing more then stories of the past peoples and idea tend to skew hitsory. People can choose to put what spin they want on an event write it down and call it history. When this happens it tends to alter what people believe and cause a major disruption to how history is preceived. Another big topic that has stopped the flow of history is racism. Amercian culture tends to leave behind or stop remembering things due to the fact that it was done by a race other then white. When this happens it really can alter more ideas of the real past then what it really has.