tldr version: Trademark law is complex, and dilution and generics are rarer than you think.
There are several ways that someone can use a trademark without the permission of the owner. The most important is nominative use, where you use the trademark to refer to the product or service itself. So, for example, if have a cocktail recipe which requires Coca-Cola, I can publish that without the permission of the Coca-Cola Company, because I’m referring specifically to their product. What I can’t do is imply that my recipe was created by the Coca-Cola Company, is approved by them, or anything else which would imply my product had anything to do with the Coca-Cola Company. This is why you’ll often see disclaimers which say stuff like “Company Foo are not related to The Coca-Cola Company. This product has not been approved by The Coca-Cola Company. Coca-Cola is a registered trademark of blah blah blah etc”, all of which makes it clear that there’s no attempt to confuse consumers.
So using a trademark nominatively doesn’t violate trademark, doesn’t require permission - and so can’t contribute towards the dilution of the trademark. Dilution is when a trademark starts to be used by different producers for different products - and that is something trademark holders are wise to defend, as if there’s sufficient dilatation you can lose the trademark. It’s not automatic, though: there’s no absolute need to defend in every instance, although wise companies always defend. At the extreme end of dilution is genericization, where a trademark comes to represent a whole category of products. However, Genericization is actually rarer than you think - many of the names which people think are generics aren’t (such as Hoover, for vacuum cleaners, or Biro for pens).
In the case of, say, someone building a text editor which supports syntax highlighting for Markdown, it’s likely that they wouldn’t need any permission from John Gruber. They’re using “Markdown” to refer to… well, Markdown, the product that Gruber holds a trademark over. It’s nominative use, and so presents no threat of dilution to Gruber’s trademark.
In the case of “Standard Markdown” though, there’s a difference: it’s a completely different product, from completely different people. This means that unless Gruber wanted to license the trademark to them, it would be a clear case of dilution if they were to use it - and so Gruber should defend it if he wants to keep the chances of dilution as low as possible. It wouldn’t automatically mean his trademark was diluted, but it would place it in danger.