It'll be fine.
I assume you "topped off" to 5 gallons in the primary? What happens is that with the trub losses and other "stuff", you often lose beer when you transfer.
Also, keep in mind that a 5 gallon carboy holds quite a bit more than 5 gallons to the top- mine is about 5.5 gallons to the top. So, if you have 4.5 gallons in there (which is likely), it looks like a lot less!
Did you take a hydrometer reading when you finished brewing? If your gravity reading was correct, the amount of beer is correct. You don't want to add water down your beer now- I'd rather have 45 bottles of great beer than 53 bottles of watered down beer!
Many of us no longer transfer to a carboy for clearing, and just leave it in the fermenter for a couple of weeks. One thing I noticed is I seem to get more beer. I think what happens is that the yeast cake and other trub items "compact" quite a bit more and I can siphon off more clear beer.
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