I'm interested in hearing more about Amazon beanstalk. Haven't personally used it. But does having my ec2 under beanstalk take care of securing my instances?
Securing your instances in what way? Elastic Beanstalk should initially provide you with instances that one would expect to be reasonably secure, but I wouldn't rely on that level of presumed security for anything important. It definitely does not provide a fully managed environment on an ongoing basis. One glaring example is that it does not handle things like OS-level security updates/patches, or provide you with instances running updated AMIs unless you re-setup your EB environment.