One reason to use the IDE might be that modern IDEs support more than simple breakpoints. For example, Visual Studio offers the following advanced debugging features:
- define conditional breakpoints (break only if a condition is met, or only on the n-th time the statement at the breakpoint is executed)
- break on an unhandled exception or whenever a (specific) ecxeption is to be thrown
- change variable while debugging
- repeating a piece of code by setting the next line to be executed
- etc.
Also, when using the debugger, you won't have to remove all your print statements once you have finished debugging.