DominoPDF supports Basic HTTP Authentication and NTLM Authentication depending on which headers the web server returns.
By using the WebUsername and WebPassword attributes DominoPDF will pass authentication details as appropriate if the authentication protocol is supported.
If you are using a protocol DominoPDF does not support you can confirm this by enabling DominoPDF logging and examining the output.
To enable logging you can add an option to the DoPDF() method as follows;
Call DoPDF(sURL, sPDF, "WebUsername=joe;WebPassword=secret;LogFile=c:\domlog.txt")