Is there a database with all known proteins/genes of specific pathogens such as Staph aureus and annotated whether it is a known virulence or resistance factor that idealy can be downloaded in table format?
I suggest that you are looking for a resource like VFDB (virulence factor database). That table does annotate by bacterial species, so you can filter as you like.
You can download a description table or FASTA sequences from their downloads page (see screenshot). Last update was 4 days ago, so they should be quite current.
Both resources include web tools for predicting the presence of the elements of interest in sequences.
If you are looking for a state of the art prediction tool for such elements in genomes, you might look into seqscreen from Todd Treangen's lab.
For a general purpose microbiological annotation and analysis resource, you might also look into BV-BRG, which succeeds PATRIC. I have only used PATRIC but BV-BRG seems very thorough.
I think that you are unlikely to find a resource that has non-virulent/non-resistance genes annotated.