Breakpoints are being hit in the Java code, the project is being run as Debug, \"Skip All Breakpoints\" is disabled, line breakpoints (blue dots) are on lines in my JSP pages.
To get debug on a JSP you might need an additional step:
Open the appropriate server in the Servers view of the Server Perspective (Window > Open Perspective > Server), and ensure that the Generate debug information when compiling JSPs (debug mode only) check box is selected. Close the server editor.
This is described in this doc: Debugging JSP files
Found a workaround. In the JSP, import a Java class and call one of it's methods. Put a breakpoint at the end of that method and step through it (F5) into the JSP.