Proteins without useful functions tend not to stay around in populations. Chances are that this protein is important for something.

If the protein is created by the combination of an ordinarily inert gene and modern environmental conditions (i.e. obesity in the modern calorie abundant and sedentary environment) then the protein would not historically have been "around in populations" and the gene would not have been selected out.

You're making a common mistake, assuming that because nature has evolved us to be fairly optimal/healthy for past historical conditions, that we're optimized by evolution in a general sense for all time; or that all we're evolved to desire is good in the present. Not so.

We're optimized for a very different world then we've created, and in many ways we're maladapted to modern living. Evolution never planned for us getting everything we want or the option to sit all the time and eat as much as we like. In fact our desires are evolved to be healthy in accordance with the scarcity principle i.e. we desire most strongly that which is both needed and scarce.

Things which are historically needed but plentiful are often taken for granted and we've evolved mechanisms to effortlessly prevent gorging on them. Take breathing oxygen for example. Gorging oneself on oxygen isn't exactly a deadly sin because its levels have been plentiful throughout evolutionary history hence we evolved to take just as much as we need. But gorging on eating was recognized as "sinful" when it became possible with the advent of agriculture and when it became necessary for culture to address the inadequacy of evolved instinct to present conditions. We've been dealing with obesity and the "sin" of gluttony ever since.