When you create a company like Coinbase, can you legally include everything the way you want in Terms of Service? I mean, if I create a company in the USA and write in its ToS that by clicking on Agree, this user confirms that she will be my slave and do whatever I ask her to do? Can I legally write that?
You can write it, but it will be unenforceable because it is illegal. However, there is no law saying centralized exchanges cannot freeze accounts or confiscate coins, and indeed this behavior is often supported or even required by various governments.
Why should an exchange reject a coin or frustrate it's flow knowing so well they will make money from the movement or trading of the coin?
To stay in the good books of the government of the jurisdiction they are operating in. They might lose profit from that user (unless of course they just seize the coins and keep them for themselves), but that's preferable to being sanctioned or shutdown.