Hi calderon,
Yes … a thicker less stretchy mattress protector can affect the ability of softer latex underneath it to some degree to contour to the shape of your body which generally “translates” into a “feel” that is a little firmer. There is more about the pros and cons of different types of mattress protectors in post #89 here. In general the thinner and more stretchy a topper is the less effect it will have on the feel of your mattress.
Other than the effect of any protector or a mattress pad you may be using … to make a mattress softer you would generally either need either a softer comfort layer or a soft topper.
Phoenix