Solution: use your ~/.my/cnf
Inside your ~/.my.cnf file define the connection parameters to your databases. For example, here I define two groups called local and toto:

[local]
user = root
password = ultra_secret
host = localhost

[toto]
user = capitaine_flam
password = galaxy
host = milky.way.net

This allow me to connect to the databases defined in the group from R using the following command:
This trick also apply when you are writing report using knitR to create Sweave or markdown reports. Your password is stored in clear in your .my.cnf file. So as long as your file system is not compromised you are fairly safe.