What is the actual invocation you are using? If the files look like nytprof.out.123 then you need to use the -f flag, e.g. nytprofhtml -f nytprof.out.123 . More details are at nytprofhtml.
It is probably also worth looking at the Apache specific docs in Devel::NYTProf::Apache as it seems not to have been mentioned thus far. (I have never used it, though).
There is also nytprofmerge if you have multiple output files and want to combine the results.