While you'll never get that last ounce of speed out of a Java program that you might be able to wring from C or Fortran, the results will be suitable for all but the most demanding applications.
As of May, 1999, the fastest VM, IBM's Java 1.1 VM for Windows, is very close to C++ on CPU-intensive operations that don't involve a lot of disk I/O or GUI work; C++ is itself only a few percent slower than C or Fortran on CPU intensive operations.
It is certainly possible to write large programs in Java. The HotJava browser, the Java Workshop integrated development environment and the javac compiler are large programs that are written entirely in Java.