Hi J.---Cows milk is highly allergenic. And yes, the proteins are the problem. A naturopath I work with advises to avoid all dairy altogether. Milk is actually not the best source of calcium. Leafy green vegetables contain more absorbably calcium that does milk, with fewer fat and calories.
I suggest you read The China Study by T Colin Campbell. Very important and valid research showing the relationship between disease rates and dietary habits, particularly animal protein consumption. You can also learn more about 'why not milk' at www.strongbones.org. This website can be accessed within www.pcrm.org. I highly recommend exploring it to learn how to optimize your health.
I have also heard that goats milk proteins are more like human milk, however, it is still not human milk and as such, is NOT recommended by Dr. Popper. That being said, I do purchase full fat goats milk yogurt at Trader Joes (best price) to have on the occasion we need a sour cream substitue or my husband has yogurt and granola for breakfast every couple of weeks.
Good luck and feel free to contact me if you have any additional questions. I work closely with this naturopath so I have lots of resources I can share with you if you'd like. BTW...I only drink water but use almond milk when I have cereal. Rice milk has more carbs so might be better for a baby. I use rice, almond and soy milks in recipes just like I would use cows milk. Have fun exploring your options. It's a great adventure.
In health, D.