What are you using to configure hibernate ? a cfg.xml or persistence.xml ?
Most likely you got it configured to use JTA which is not available when running inside Eclipse.
The simplest workaround for this is to not use such config from within eclipse. You can still keep using your config files and just have a single properties file to override any JTA/Server specific settings.
Try create a seam project and see the hibernatetools-console.properties that generated there and associated with the hibernate console configuration - it should do the trick.