Personally, I don't use automation for a lot of reasons. However, if you want to use it, go to the options screen and check the option Workers Will Not Replace Improvements (that is not the exact correct wording for the option but I don't recall it at the moment and it will be similar enough to be obvious when you see it). With that option on, automated workers will not replace your mines, cottages, farms, etc. with forts but they will still build forts on unimproved resources, because this allows access to resources. My guess is that it was simpler to have them do that then for the programming to analyze which improvement would be best. If you don't want them building the forts instead of the specific resource improvement, don't automate.