There are four major reasons...
1. Environmental impact of silicones;
2. Environmental impact of the manufacturing process;
3. Dislike skin or hair feel; and
4. Unavailability of products.
ENVIRONMENTAL IMPACT OF SILICONES
I didn't think about the environmental impact point, so here's a little research I've done...
From the Polymeric Materials Encyclopedia: "A generally accepted conclusion is that methyl silicates and silicone polymers have no known negative environmental impact." (I'll summarize it briefly here, but I suggest you read the article as it is really interesting!) The low molecular weight silicones are so volatile they undergo an oxidative degradation in the atmosphere, completely degrading into water, silicic acid, and carbon dioxide. The higher weight silicones will end up as sludge in waste water treatment plants, but will degrade when used as fertilizers to water, silicic acid, and carbon dioxide.
From The Principles of Polymer Science in Cosmetics and Personal Care: (Summary) Due to extremely low water solubility and high vapour pressure, silicones are not found in any appreciable extent in soil or water, and they may actually reduce the creation of ground ozone. They don't contribute appreciably to the creation of greenhouse gases. Toxicity to water creatures is limited and the corresponding risk is low (they really don't define what these words mean...)
I found a press release from Dow Corning talking about the environmental impact of silicones, but I'm excluding this one because it is going to be self-serving.
From Silicone Surfactants: I swear they read and summarized the Polymeric Materials Encyclopedia, but they pretty much say the same thing as that book...which apparently came from a study entitled "Final Report from Statewide Air Pollution Research Center, University of California, Riverside, to Dow Corning Corp., November 1992.)
So on the surface it would appear that silicones are considered safe for the environment.
ENVIRONMENTAL IMPACT OF THE MANUFACTURING PROCESS
What about how they are manufactured? So far I've found nothing...apparently it's a proprietary process and no one will share the information.
SILICONES ARE OCCLUSIVE
Not brought up here, but something I noticed on other sites...Silicones are occlusive, and they are using this word as a pejorative. (Please visit the post on occlusives for more information). I like occlusives - I like to trap in the goodies next to my skin. This does not mean my skin isn't breathing - skin doesn't breathe! - and I don't see the same comments made about cocoa butter or allantoin. Perhaps because the sites I found that make these statements are trying to sell you on their version of all natural. My opinion - yes, dimethicone can be an occlusive and is approved by the FDA as same, but I like this feature!
SKIN OR HAIR FEEL
Yes, they can weigh down your hair, and I've noticed (anecdotally) that too much cyclomethicone makes my hair feel greasy, so really that's a personal choice that comes down to skin or hair feel.
UNAVAILABILITY OF PRODUCTS
If you can't get them, then that's going to limit your use! I know there are so many surfactants or exciting water soluble oils I want, but ordering from the States just costs too much with the high minimum orders, the shipping, the duties, and the like.
The lovely thing about making our own products is we can choose whatever philosophy we want and we shouldn't have to explain ourselves as long as our products are preserved well, protected from rancidity, and formulated with our ingredients used in safe levels. (If you're selling things and making claims, then I'm going to demand an explanation!) I ask the questions I do because I'm interested in the philosophical bent of others - I can't learn if I don't ask. So thanks so much for your contributions to this question - it made me think! And I love thinking (little girl likes brain!)
My quote of the week from Alex Trebek (courtesy of A.J. Jacobs in "The Know It All") - "I'm curious about everything. Even things that don't interest me." From me...how can I know I'm interested in something if I don't ask?
What's the next question? Any suggestions?