Assalaamu alaykum. Amazon.com works by allowing you to register a seller account on the site, whereby you can list products which you want to sell on Amazon. Once the customer orders your product on Amazon, the money paid by the customer is transferred into the seller account while a part of the money is deduced by Amazon for listing your product. Then Amazon notifies you via mail that the product has been ordered and so the shipping needs to be done. The seller now has the option of getting his product shipped either through 'Amazon shipping services', wherein Amazon gets the sellers product picked up and shipped directly to the customer, OR the seller may get the product shipped through a shipping company of his choice. Whether Amazon uses third parties for shipping - I have not done research on that. Once the product is delivered and acknowledged by the customer, Amazon transfers the money from the seller's account on Amazon to the actual bank account of the seller. It is then that the seller actually gets his money. For further details and cross-verification, I request you to visit Amazon.com. I have the following questions:
1- So Amazon earns by taking a certain amount once the product has been sold - is this halal?
2 - Is the way in which the seller earns halal or not?
3- If anything is haram in the above summary, please provide any halal alternative methodology for if one actually wants to set up his own online store like Amazon. If nothing is haram, then please ignore this question.
Thank you for your time.

All perfect praise be to Allah, The Lord of the worlds. I testify that there is none worthy of worship except Allah and that Muhammad, sallallahu ‘alayhi wa sallam, is His slave and Messenger. 

If the seller owns the product that he lists on the website, then there is no harm in the mentioned transaction regardless of whether he ships it to the customer through the website or through any other shipping company. There is also no harm in the fees that the website charges for listing the product, or for acting as an agent for the seller in selling the product and receiving the price, or as an agent for the customer in receiving the product and sending it to him, or only to promote the product and list it on its pages while the contract is conducted directly between the customer and the seller. None of this affects the validity of this transaction. Hence, the important factor here is that the seller must own the product that he is listing on the website.

Allah knows best.