1) Java is a language. While webMethods is a tool. webMethods provides lots of build-in services as loke the 

API in java.For using the API, in java again we need to wrie some codes.But in webMethods they are providing the drag and drop 

facilities. so its a time consuming process.

Apart from this webMethods supports lot of functionality like publish\subscribe, portal developement, brokers etc...

2) When you can walk, why you need Bike? or if you've bike, do you need car?

Java is a language while webMethods is specialised tool with many built in functions/feature to support guaranteed

deliveries, transaction tracking, resubmissions, data transformation, SOA, Event Management, web service, File,

EDI, JDBC, SAP, JDE, JMS, MQ Series, integration with multiple applications on multiple platform. 

If you'd to do all of that by yourself in Java, you'll look at years to develop full proof solution that webMethods can

provide you out of box. As they say, don't reinvent the wheel.