If you have a Commercial / Professional license with MATLAB Compiler, then you may distribute the .exe for profit without any royalities to MATLAB.
If you have an Academic license with MATLAB Compiler, you would only be allowed to distribute the .exe for the internal purposes of your institution; to distribute it outside your institution would require a Commercial / Professional license.
The strictest rules in all of this have to do with distributing MCR. For sufficiently new versions, your end users can get an appropriate MCR version from Mathworks (a bit of a nuisance for them), so you can distribute your software without MCR and rely on your users getting MCR (which they will probably find an unpleasant exercise.) But if you wish to distribute MCR with the software, or if your Compiler is sufficiently old that the MCR is not made available from Mathworks and you must distribute MCR, then there are rules that you need to dig out of your license.txt file;
web(fullfile(matlabroot,'license.txt'))
The last time I looked, it was not permitted to make MCR publicly available, that you had to control access to it such as with a password system. Maybe they made it easier.
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With regards to license protection of your application: Mathworks does not supply any tools for that. You can invent your own schemes or you can lease rights to use a commercial protection scheme. Many of the larger software packages use FlexLM, including MATLAB, Maple, and Mathematica, but it might be more complicated than you need or more expensive than is worthwhile for your software. I find a number of other tool providers when I do a brief search.
