I suppose there's a whole list of reasons a particular manga might not have an anime. We first have to look at it and ask if the creator even wants their work to be made into an anime. It's not impossible that they believe that what they're trying to do is best represented as a manga. We can look at both Junji Ito's stuff and Beserk for great examples of when making something into an anime might lessen the impact of a story. Both Beserk and Ito's stuff are so heavy on their artistic details that a case could be made for not transferring them to a medium they aren't suited for. It may not be the exact same thing, but it's definitely worth thinking about author intention. We can look at Jojo's Bizarre Adventure as a manga/anime that took years to get turned into a long running anime series because the creator specifically held off on doing so.
There's also just the plain fact that not every great manga will get made into an anime. For every anime that gets made there's ten more mangas and light novels jockying for a shot at being one. Even popular anime often wait years and years before getting made into one. It's all about what executives think is going to sell, not on what fans think should be made. Every anime out there is a super expensive and time consuming process, so the only things getting made into anime are safe bets.