I hope the following answers your question; if not, you will need to be more precise. I know FontLab only very superficially but I don't think it generates anything else than what you designed.

Here is what you seem to be experiencing. On OS X and on Windows, TextEdit, Word, Pages, Powerpoint (standard Mac and Windows applications) use a "fallback font" when the current font is missing a character. To avoid that you need an application that does not rely on the fallback mechanism. I know that Adobe InDesign would not replace your missing glyphs by those of a fallback font. If you are on a campus with a fast connection, you can install texlive 2013 (on the Mac, it is MacTeX, on the PC, TeX Live). It comes with XeLaTeX that does not use the fallback mechanism either. Here is how MacTeX looks (with TeXShop); first the input file:

and now what I get after clicking "Typeset".

The font does not contain Hebrew characters and they are displayed as missing.

You could also try LyX, that is built on top of TeX and is supposedly more user friendly.

Of course, texlive also runs on Unix.

Once texlive is installed, you also have lualatex. If you have any doubt about the glyph list in your font, here is a lualatex script that will give it (from the manual)

--- file lglyphs.lua --- cut here
#!/usr/bin/env lualatex

local f = fontloader.open(arg[1])
local i = 0
while (i < f.glyphmax) do
  local g = f.glyphs[i]
  if g then
    print(g.name)
  end
  i = i + 1
end
fontloader.close(f)
--- cut line ---

Then

lualatex lglyphs.lua fontfile

will give you the glyph list in your font file. You can make that file executable and run it as a unix script but on my mac it needs the extension .lua to work.

FontLab is only generating the fonts you create. The other glyphs you see being displayed in software are fallback fonts, i.e. the default fonts used by that software to display characters that are not supported in your font.

The Unix script can be called lglyphs without the .lua extension if the first line is replaced by

#!/usr/bin/env texlua

and will then execute properly. Other options can be found in the manual at http://www.luatex.org/svn/trunk/manual/luatexref-t.pdf