First, to be clear, the Webmaster Tools notifications are just that. Google isn't indicating any kind of a problem, Erik. It's just declaring what it has found in the site's robot.txt file.
There's no way to give a definitive answer without seeing the actual website structure, but in general, it is VERY common and good practice to no-index the categories and tags on CMS-based websites. Usually, you want some form of the archives to be indexed, but it's usually the individual pages that are most important. (e.g. not date-based archives.)
The problem with allowing all of these to be indexed is that to a search engine, they will all look like duplicate content of other pages on the website. This will cause the search engine crawler to have to work much harder to find all the content on your website, and ad a result may quit part way though.
In addition,much of the content it finds it will consider to be duplicative of other pages on the website, and therefore will have a hard time knowing which version is actually the most valuable result to return. And as a result will split the authority of each of the pages, making them MUCH harder to rank.
This is a standard challenge of any CMS based website, because they display the same content organized by what are referred to as different taxonomies (different ways of categorizing or linking the same information).
Again, without seeing the actual site I can't say for sure, but short answer is that those three directives are very common for CMS- based websites and are very likely correct.
Hope that helps?
Paul