AWS is a suite of services. One of those is EC2, which is just virtual servers hosted by Amazon/AWS. A virtual server is no different than a physical server from the perspective of the guest operating system, regardless of if it is Linux or not. Linux is just the software running on the server, it has nothing to do with ownership. The only way "running on AWS" is problematic is if you tied yourself to their non-generic services like ECS or Beanstalk.
tl/dr: building on AWS and building on Linux are not mutually exclusive. One represents hardware the other software.
We used AWS and EC2 at my last job so I've done about 4 years worth of what you're describing. Definitely if you use Amazon as your way of getting a Linux instance that's fine, because then you can just move to Linode or any other hosting service because Linux is the one thing they all support.
When I say don't use "AWS" I should've been more clear I'm talking about their proprietary stuff. Basically you should be able to run on a plain Linux as your base.
