An example of a free-software violation would be the bittorent clients, which have to way to disable obeying the private bit. While one does have access to the source code, and can therefore modify this themselves, the software is designed with the explicit intention to remove the users freedom to dis-obey the private bit.
Adds are annoying, but do not affect any user freedoms.
EDIT: Discussion on ubuntuforums: http://ubuntuforums.org/showthread.php?t=2060764
Here is a quote of a quote of the technology director of Canocial:
"Another addition is that we will be including Launcher web apps icons to Amazon and the Ubuntu One Music Store by default. We feel that these icons will provide convenient access to these resources for our users and also benefit the project with the generation of affiliate revenue in those cases that these resources are used. If our users choose to not use these Launcher icons, they can be easily removed by the user by dragging the icon to the trash."
I got that from the linked forum, but haven't searched the mailing lists to validate it.