When the pattern "X stands out as Y" is used in English, it means that there may be many things that do Y, but X is among the things that do Y the most or the best, etc. Like the leader of a group may literally stand out in front of the group she leads, X stands out as a leader among the things that do Y. In the specific example, X = Universities and Y = "places that really are about the authority of ideas". So the paragraph claims that Universities are leaders among places where ideas are generated.

Something that "stands out" is easy to notice, or visible. The mental image is of people standing together in a crowd, and one person who is standing "out," or apart from, the rest. It would be helpful if you would give your source and more context. It appears to be a talk by former Harvard president Larry Summers. The talk is entitled "The Authority of Ideas." I found it here: http://floatinguniversity.com/summers-transcript He is talking about kinds of "places," by which he means institutions--governments, corporations, churches... and universities. He says universities "stand out." They are apart from the others. They are different from the others. In most institutions, individual people have authority. If the CEO of McDonald's corporation decides that their hamburger buns will be made without high-fructose corn syrup, they will be made without high-fructose corn syrup--because the CEO has the authority to say so. Summers says that universities are different. At universities, ideas have authority, rather than people. A professor does not have personal authority because of holding the position of "professor," it is the logical clarity of his ideas that carry authority. He further says that universities are "about" the "authority of ideas;" the concept of "the authority of ideas" is really what makes a university a university. (He also indicates, in the last paragraph, that he thinks the world would be a better place if other institutions were more like universities).

Simply means, universities give big or rather best ideas