Misdee my understanding is that it's made from cows milk but the proteins that cause a reaction are broken down to allow for digestion by those with problems. Nutramigen is broken down into a few pieces and Neocate is broken down into one molecule. That's how DD's paediatrician described it anyway.
My ds2 was on Pepti Junior and just as I successfully weaned him from BF to that (at 12 months), on his birthday he had an allergic reaction to that as well ! (Pepti Junior is similar to Nutramigen but Nutramigen is based on broken down (hydrolysed) casein whereas Pepti is based on hydrolysed whey). He's now on Neocate Advance (unflavoured) - he refused to entertain the flavoured version , which is available for over 1's. We gave him Infasoy whilst getting him onto the Neocate, which took about 2 weeks in total.
There are issues with soy formula though and phyto-oestrogens in little boys, but nothing which is really proven just a fairly limited study in primates. Also as Sunshinemummy says, many dairy allergic children are also sensitive to soy (and I think soy is a "worse" allergy than dairy in terms of avoiding soy products and likeihood to grow out of it).