Because the links like the edu text links fit in quite unobtrusively into the web page they are not marked by the search engines for exclusion. Of course such links do not include the Google Adwords ads that can be seen by the search engine quite automatically.
Other ads are much more prominent than the text links and they can be easily identified and banished. On the other hand it is extremely difficult to distinguish between the genuine hyper links and purchased text links on the web page and that is why mostly the search engines do not ignore such links even if it is bought and not the genuine hyper linked one.
The scenario may change with advanced technologies coming up or with some other web related developments in future. But for the time being the text links continue to dominate the scenario where users aspire for search engine optimization using links. It is true that the objective of search engines is to produce results relevant to the search without being influenced by the money paid for the purpose but as already pointed out such distinctions are difficult to find out.
If you are thinking of buying text links of some type to enhance your search engine optimization process you may consider buying links that could really help in your endeavor being commensurate to all requirements of genuine hyper links.