A VPN provides confidentiality from the VPN entry point to the VPN exit point. In typical enterprise scenarios where you're using a VPN on your laptop to connect to your enterprise network from a public or client network, the VPN keeps your data confidential between your laptop and the VPN server in your enterprise network; it doesn't do anything for the part between the VPN server and the site you're connecting to.
+-------------------------------------------------+
| enterprise network |
+--------+ | +------------+ +--------------------+ |
| laptop |<==============|===>| VPN server |<----->| application server | |
+--------+ VPN | +------------+ +--------------------+ |
| |
+-------------------------------------------------+
I can't tell from reading your question whether this is the scenario you're asking about. If you have an enterprise network with several physical locations and a shared VPN between them, then that VPN protects the communications between the VPN servers at both ends but not inside one location. Generally speaking, a VPN protects the communications only between the points on each side where the encryption is performed.
Note that the VPN only protects the traffic that goes through it. Depending on your configuration, DNS traffic may use the ambient network rather than the VPN; this can improve performance but it means that whoever can snoop on the host network can know which sites you're accessing (but not the data that you're exchanging with them).
The most common form of point-to-point confidentiality is SSL/TLS. An SSL connection keeps its data confidential between the client and the server (though it can sometimes leak information through timing). You'll usually see SSL in the form of HTTPS when connecting to websites, but it's also used to secure other applications such as IMAPS (IMAP over SSL), SMTPS (SMTP over SSL), …
All forms of point-to-point confidentiality assume that you're talking to the right server: it's no good having a secure connection if the guy at the other end is an attacker performing a man-in-the-middle attack. SSL rules out man-in-the-middle attacks through certificate verification, and its correct behavior depends on an operation that has to be performed by your browser for every site. Usually your VPN only connects to one end point and will be set up to reject such hijacking attempts from the start, so in this respect a VPN does provide a little extra security, but only at your end of the connection.