How do I handle this professionally? Should I just let it go?
There's really little you can do here. You most likely either have to get over it, or move on to another company and hope that they don't do reviews the same way. It might give you some comfort to know that what you have experienced isn't directed just at you, and isn't at all unusual.
Some companies (particularly very large companies), set a budget for the upcoming year, and use the annual review process to slot employees into that budget. And many companies use the "rating" as the mathematical factor which determines your annual raise.
In recent years, I've been given an increase budget of 3%. I have to make my entire team's budget come out to 3% more than the previous year - even if every single individual on the team had an outstanding year and each deserve more than 3%.
If I wanted to give someone more than 3%, I had to take the money from someone else. I was not given a choice. And the mechanism at my company was such that I had to adjust the ratings, so that the raise percentage came out correctly. If I didn't do the adjustment, it would be automatically kicked up to my boss. My boss would then adjust it, and reprimand me for not doing so myself.
I know - that's a foolish system, but it is what it is, and middle-management has to just suck it up and deal with it, and hope that they don't completely disillusion too many good people.
In your case it's quite possible that your direct manager either didn't know about the overall departmental requirement, didn't care, or wasn't instructed to deal with it at your level. Thus, the realignment to fit into the budget was passed up to the next level, and they did what they have to do.
You could complain to your boss about the unfairness, but most likely she already knows about it. You could complain to her boss, but again they all most likely understand but are powerless to do anything about it.
For the future, you can only strive to be the best employee in your group. That might get you a bigger slice of the (limited) pie.
Since you indicate that this is the first year you have had this happen to you, you might want to think about what is different from past years. Has your work compared to your departmental co-workers not been as good as it had been previously? Is the overall budget for this year more constrictive than in past years? Has the company changed their process for handing out ratings? Do you have a new boss, or is her boss new (and perhaps not willing to adjust ratings in your favor)?
Lastly, how should I word my comments on my review when I sign it? I
want to make sure it's noted that I disagree but again, I worry about
it not being professional enough.
Well, if it makes you feel better, you can note in your comments that you think you are deserving of a higher rating, and why. Careful wording can make sure that it isn't unprofessional. I've always encouraged folks on my team to use the comments this way if they chose to do so, and never took offense if they vented their anger in their comments.
But honestly, having been on the management side of this exact scenario many times, your comments are extremely unlikely to have any affect (other than perhaps making you feel better). Your boss will read them. Your bosses boss might or might not read them. HR probably won't read them. Nobody is likely to act on them.