Yes, the allergies could quite possibly be causing his ears to hurt. This is because of the way that kids, and all of us, are built. The back of the nose, where all of his mucous and allergic products hopefully drain, is also the place where the ears drain. The ears drain through the eustachian tube into the same area, and so the openings of the tubes are subject to the same allergens that the nose is subjected to. As they are lined with the same tissue as the nose, they will also react in a similar manner, meaning that they will swell. Additionally, the chronic inflammation of having snot pour over the opening will make them swell even more. Finally, kids have bigger tonsils and adenoids (which adenoids also lie at the back of the nose and can often obstruct the outflow of snot, making it drain out the front). When allergies happen, the adenoids are also prone to swelling for the same reason. Whether because of inflammation at the opening or inflammation causing the adenoids to swell, the end product is obstruction of the eustachian tube opening, which leads to fluid backing up in the ears, causing aural fullness and pain. Please speak to your doctor
about your problem and ways to fix it.