Both Java EE and Spring provide a huge amount of functionality and do it in an uniform way, so you don't have to glue lots of different libraries together. They aim for enterprise world, where this functionality is required. Not every project need it, so sometimes it might be not necessary. IoC is awesome on huge projects, but if your project is 10-20 classes, it's just unnecessary abstraction. Distributed transactions increase robustness, when you're working with multiple databases and message queues, but if you're creating website with a single database, you just don't need it. WebServices implementation is a must, when you have to integrate with someone, who's exposing their API via webservice and you'll drown in details, if you'll try to implement it manually, but if you're using lightweight REST APIs, it's quite possible to do it without any frameworks.

So it's good when you need it, and it's unnecessary over-engineering for simple projects.