Law enforcement went fishing in Gedmatch, and that scared many people off. After an uproar about the lack of informed consent, the database owners opted everyone out and everyone is now required to opt in. So those people who were deceased at the time this happened, or haven't logged in for a long time, no longer have their DNA in the public pool.
The concerns about law enforcement using the database are quite varied. I find that those who don't care about LE being there dismiss the concerns of those who are concerned, and it's not all about covering up a crime. There are a number of issues. Some people who manage multiple kits are also taking it upon themselves to make decisions for their test takers, and removing the right of informed consent from their test takers. My personal code of ethics means that every time there has been a change involving privacy at Gedmatch, I go back to my test takers and obtain their consent again. Eventually I couldn't be bothered so I just deleted the kits from there. I've also noticed that a lot of my matches have deleted their trees from Gedmatch since LE started using the database, so Gedmatch has lost its value for me.
Many of the matches that I have at other sites have an extremely limited understanding of how to interpret matches. Ancestry provides a nice interface, it has ThruLines to help them (it's of limited use to some people due to the junk in their relatives' trees, but I've been really lucky and it works very well for me). It has ethnicity information and this is all many of Ancestry's customers want. To use Gedmatch well, it requires a greater understanding of the underlying science, therefore it will appeal to a smaller group of people. It is probably also of greater appeal to those who can afford to buy kits to test numerous relatives.
