You can put the arguments in quotes:
myprogram.exe "(this is some text, with special characters.)"
Though I wouldn't assume that parentheses cause problems unless you are using blocks for conditional statements or loops in a batch file. The usual array of characters that are treated specially by the shell and need quoting or escaping are:
& | > < ^
If you use those in your regular expression, then you need quotes, or escape those characters:
myprogram "(.*)|[a-f]+"
myprogram (.*)^|[a-f]+
(^
is the escape character which causes the following character to be not interpreted by the shell but instead used literally)