به = to ____ به ایران خوش آمدی = welcome to Iran. در = in ____ we can't say welcome in Iran. so در ایران خوش آمدی is wrong.

I suggest that you do not waste your time to find a rule for propositions. It is what you called I think سماعی in Arabic. You have to use it like the native people. There are lots of such things in Arabic too. For example, can you tell me why the plural of طیبه is طیبات but the plural of شجره is اشجار not شجرات.