If you have significant infrastructure in multiple cloud providers, colocation facilities, etc then it's very possible you want to keep your OS and configuration management systems consistent between all of them.
Amazon linux also comes pre-installed with a number of agents that a significant infrastructure may not want to have running at all times. So between releases you must determine what you want to strip from Amazon linux.
Additionally, if you build your ec2 AMIs in your CI/CD pipeline that becomes more annoying with Amazon Linux than it is for centos/debian which have clear unattended install paths.
Additionally, you may be significantly invested in your distro such that changing at any time takes a lot if effort and Amazon linux's releases are less predictable than other distros so if they go down a problematic direction for you, it could cost you a lot of effort to migrate.
Thinks like the ubuntu ec2-optimized AMIs are also no less optimized for ec2, and honestly Amazon linux's kernel these days is hardly different from any others in terms of performance. They apply a moderate patch set, but it's typically for early support for new instance types or just drivers. For example, some patches for their ARM hardware, or their ENA driver or lustrefs for their fsx product. All of these patches get upstreamed too. On top of their kernel, they have ec2 autotune which is a tiny python project that tunes like 10 sysctl that your config management system can easily handle (and may fight with).
Anyway, I agree that for small projects running in only AWS I think amazon linux is a great choice and potentially the best choice, but at larger shops I'm much less convinced. Although, even at smaller shops I think a lot of people are just more comfortable with ubuntu, there's a guide for just about anything on ubuntu, and pretty much no software that doesn't target ubuntu.
We operate about 10,000 servers in EC2 so I keep up with the Amazon kernel patches and apply the relevant ones to our internal kernel build for CentOS, but don't otherwise really look to the rest of amazon linux much