You need to modify the FLAGS in "config.status" which autoconfigurates the makefiles of all the applications in tesseract-ocr.
Add -pg to CFLAGS,CXXFLAGS, and CPPFLAGS and then tell me how it works.
Coincedentally, I'm also trying to profile tesseract with gnu gprof, except in my gmon.out I'm seeing that there is only one function in the call stack with 0s. I'd like to know if your result is any different, let me know how it goes.