**EDIT: Sorry, for some reason I thought you were talking about the stomach, have no idea why, must've been drunk.
Fermentation will occur in the colon, but this is mostly the bacteria digesting the fibre. Also by the time this gets to the colon the sugar and vitamins have ALREADY been absorbed by the small intestine, hence any nutritional gain from that fruit has already taken place. This means the sentence " the fruit will ferment in your gut and you will not reap any nutritional benefits from the fruit" is nonsensical.
Furthermore the fibre from fruit will ferment in your colon whether you consume it with protein or not.
So yeah this is just another retarded internet rumour.
Anyway, I think you might find this interesting as it shows consuming some fruits can affect protein digestion (which is sort of visa versa to the scenario you were suggesting, but it may be the origin of this myth):
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The inhibitory effects of berry polyphenols on digestive enzymes.
Biofactors. 2005;23(4):189-95.
Abstract
The evidence for the effect of polyphenol components of berries on digestive enzymes is reviewed. Anthocyanins inhibit alpha-glucosidase activity and can reduce blood glucose levels after starch-rich meals, a proven clinical therapy for controlling type II diabetes. Ellagitannins inhibit alpha-amylase activity and there is potential for synergistic effects on starch degradation after ingestion of berries such as raspberries and strawberries, which contain substantial amounts of ellagitannins and anthocyanins. A range of berry polyphenols (e.g. flavonols, anthocyanidins, ellagitannins and proanthocyanidins) can inhibit protease activities at levels which could affect protein digestion in the gastrointestinal tract. In contrast, potential for the inhibition of gastrointestinal lipase activity, a proven therapeutic target for the control of obesity through reduced fat digestion, may be limited to proanthocyanidins. Taking into account the manifold possible synergies for inhibition of starch, protein and/or lipid digestion by the spectrum of polyphenol components present within berry species, the inhibition of digestive enzymes by dietary polyphenols may represent an under-reported mechanism for delivering some of the health benefits attributed to a diet rich in fruit and vegetables.
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The issue with the above is: Dietary polyphenols in some fruits -> inhibition of proper protein digestion -> colonic protein fermentation -> potentially carcinogenic products.