There are 5HT-3 (serotonin type 3) receptors in your gut that are responsible for nausea and vomiting. Various psychedelic drugs are supposedly selective for the 5HT-2A receptor that is implicated in mind-alteration, but there is usually some amount of overlap in receptor affinity. By stimulating the 5HT-3 receptors, the drugs cause a feeling of nausea and can cause vomiting.
Also note that the RoA does not seem to affect this-- IV, nasal, and rectal administration of 2C-E can show similar or increased nausea as oral ingestion of an equipotent (corrected for increase in potency by RoA) dose. Once the drug is in your bloodstream, it is stimulating all the receptors it possibly can, all over your entire body. Speed of onset also seems to affect nausea, with faster RoAs (IV, nasal) giving more chance of puking.
Some people are able to meditate or do chakra exercises to "channel the energy" that may also be somewhat psychosomatic in nature. In general, if you have nothing to do but sit on a couch and think about how much your tummy hurts, your highly enhanced psychedelic mind may go off on a bad trip about that gut pain. Distraction by way of positive activities (shower, dance, play, etc) can have a tremendous effect on the physical side-effects noted.
YMMV, but for me personally, 25mg diphenhydramine (benadryl, unisom) taken concurrently with oral 2C-E decreases the nausea substantially. The sedative effects of the antihistamine are not noticed through the stimulation of the 2C-E.
Herbal tea (peppermint, ginger, lemon, chamomile, honey, etc) also does wonders for relaxing the mind and body.