The Java ecosphere is more about choices than the .net one is. There often enough is not the one standard way of doing things. This is why tools can't only present one way. You need to know what you want and choose the tools accordingly. You can select your persistence, presentation, DI, whatever. There are different accepted solutions.
But: If you want to do "standard"
J2EE in an integrated packet, then for beginners Netbeans offers a complete solution including an app server (Glassfish, but you can install the web container Tomcat automatically, too). I guess this is what you are looking for. Download, install, create new project, run. Plus a few wizards and tutorials helpful for beginners.
With Eclipse you need more setup (some plugins, integrating an app server, even if it is only a three click act) and need to know better what you want and what you are doing. Not that well suited for beginners to the Java ecosphere (but there may be other reasons why the market share of Eclipse still is higher).