|Linux Advanced Routing & Traffic Control HOWTO|
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As of Linux 2.4.14, bridging and iptables do not 'see' each other without help. If you bridge packets from eth0 to eth1, they do not 'pass' by iptables. This means that you cannot do filtering, or NAT or mangling or whatever.
There are several projects going on to fix this, the truly right one is by the author of the Linux 2.4 bridging code, Lennert Buytenhek. He recently informed us that as of bridge-nf 0.0.2 (see the url above), the code is stable and usable in production environments. He is now asking the kernel people if and how the patch can be merged, stay tuned!