They can be compared to an extent. It is a numerical value to express how good a player is at what they do. What Madden is telling us is that Sherman is better at CB than Thomas is at safety. I don't believe that.
I also think it is no coincidence that the loud mouthed sherman gets the coveted 99 while the more reserved Thomas does not. I think it is evidence of how the ratings are becoming more involved in a marketing standpoint.
Also, if the overall for safeties is too heavily tilted towards coverage skills that makes Thomas' rating even more questionable.
Having said all that, I actually don't care all that much lol