Its about money. With your iPhone example, they are forced to stick with (I think) Verizon and AT&T, in which the both of them pay Apple a fraction of to stay exclusive too. For other companies to make profit off the iPhone without paying Apple a percentage of the profits, you can guess that's upsetting. As well people obtaining software other than from/through them means they loose profits. As long as the Apple phone is the way they design it, they can continue selling you what they want, but if people customize it to what they want, getting rid of the need to give apple money...
I really hate the
crap and
bullpocky their pulling, trying to overturn "legal purchasing of a product and it's accessories transfers ownership and legal authority of, to the consumer" by making jailbreaks/modifications illegal and punishable by law.