Did you extract the correct dirver jar file from the binary distribution Zip file? You need a file named mysql-connector-java-[version]-bin.jar.
From the connector-j.html page in the MySQL /docs folder:
Update: The com.mysql.jdbc.Driver did not work with connection pooling enabled but the com.mysql.jdbc.jdbc2.optional.MysqlConnectionPoolDataSource driver does work (see below)
Connection Properties
Transaction Type: LOCAL_TRANSACTION
DataSource Class: com.mysql.jdbc.jdbc2.optional.MysqlConnectionPoolDataSource
serverName localhost
user root
password <password>
Retype password <password>
databaseName <MySQL database name>
portNumber 3306
networkProtocol <empty>
Other Properties <empty>
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#Adapters-and-E-Standards#webMethods#Integration-Server-and-ESB