My view on using VLANs for security
I've recently read some criticism of the security value of VLANs. Since we use VLANs heavily I've been thinking a bit about this issue and today I feel like writing up my opinions. The short version is that I don't think using VLANs is anywhere close to being an automatic security failure. It's much more nuanced (and secure) than that.
My overall opinion is that the security of your VLANs rests on the security of the switches (and hosts) that the VLANs are carried on, barring switch bugs that allow you to hop between VLANs in various ways or to force traffic to leak from one to another. The immediate corollary is that the most secure VLANs are the ones that are on as few switches as possible. Unfortunately this cuts against both flexibility and uniformity; it's certainly easier if you have all of your main switches carry all of your VLANs by default, since that makes their configurations more similar and means it's much less work to surface a given VLAN at a given point.
(This also depends on your core network topology. A chain or a ring can force you to reconfigure multiple intermediate switches if VLAN A now needs to be visible at a new point B, whereas a star topology pretty much insures only a few directly involved switches need to be touched.)
Because they're configured (partly) through software instead of purely by physical changes, a VLAN based setup is more vulnerable to surreptitious evil changes. All an attacker has to do is gain administrative switch access and they can often make a VLAN available to something or somewhere it shouldn't be. As a corollary, it's harder to audit a VLAN-based network than one that is purely physical in that you need to check the VLAN port configurations in addition to the physical wiring.
(Since basically all modern switches are VLAN-capable even if you don't use the features, I don't think that avoiding VLANs means that an attacker who wants to get a new network on to a machine needs the machine to have a free network port. They can almost certainly arrange a way to smuggle the network to the machine as a tagged link on an existing port.)
So in summary I think that VLANs are somewhat less secure than separate physical networks but not all that much less secure, since your switches should be fairly secure in general (both physically and for configuration changes). But if you need ultimate security you do want or need to build out physically separate networks. However my suspicions are that most people don't have security needs that are this high and so are fine with using just VLANs for security isolation.
(Of course there are political situations where having many networks on one switch may force you to give all sorts of people access to that switch so that they can reconfigure 'their' network. If you're in this situation I think that you have several problems, but VLANs do seem like a bad idea because they lead to that shared switch awkwardness.)
Locally we don't have really ultra-high security needs and so our VLAN setup is good enough for us. Our per-group VLANs are more for traffic isolation than for extremely high security, although of course they and the firewalls between the VLANs do help increase the level of security.
Sidebar: virtual machines, hosts, VLANs, and security
One relatively common pattern that I've read about for virtual machine hosting is to have all of the VLANs delivered to your host machines and then to have some sort of internal setup that routes appropriate networks to all of the various virtual machines on a particular host. At one level you can say that this is obviously a point of increased vulnerability with VLANs; the host machine is basically operating as a network switch in addition to its other roles so it's an extra point of vulnerability (perhaps an especially accessible one if it can have the networking reconfigured automatically).
My view is that to say this is to misread the actual security vulnerability here. The real vulnerability is not having VLANs; it is hosting virtual machines on multiple different networks (presumably of different security levels) on the same host machine. With or without VLANs, all of those networks have to get to that host machine and thus it has access to all of them and thus can be used to commit evil with or to any of them. To really increase security here you need to deliver fewer networks to each host machine (which of course has the side effect of making them less uniform and constraining which host machines a given virtual machine can run on).
(The ultimate version is that each host machine is only on a single network for virtual machines, which means you need at least as many host machines as you have networks you want to deploy VMs on. This may not be too popular with the people who set your budgets.)