OK, I'll try this again. One point-this does break down for a 1st level druid, because a 1st level druid is allowed to have twice his hit dice in animal companions whether adventuring or not. (This is probably a bad idea, because of the experience point issues you're bringing up, but it sure helps keep those 1st level druid PC's alive.

)
There are specific guidelines in the DMG for increasing or decreasing experience point awards based on the difficulty of the encounter. Dealing with a sedentary druid in her lair, including twice her hit dice of animal companions (not to mention the snares, magical protections, and home-ground terrain familiarity) certainly warrants at least a 50% (and possibly a 100%) increase in the experience award for the encounter.
So, a sedentary 6th level druid with her two brown bear companions would normally be worth at least 2700 and possibly 3600 experience points to a 6th level party-as much as three or four brown bears by themselves.
A normal, adventuring 6th level druid is CR6, and has one CR4 brown bear companion. She is worth 1800 experience points under normal conditions, as much as two brown bears by themselves.
I fully agree that this is seems out of whack-the druid (herself) is worth more than a brown bear by itself. My point is this-the druid
cannot possibly be under-valued by this system. A PC party of four 6th-level druids meeting an NPC party of four 6th-level druids (each with their respective animal companions) is a toss-up match (obviously, right?), so the individual 6th-level druids
must, by the definition of the CR system, be a CR of 6
with their animal companions included. If you bump the druids up to CR8 because of their companions, then you have to conclude that two 6th-level druids are a deadly threat to a party of 4 6th-level druids. But then, one 6th-level druid must be a deadly threat to the two 6th-level druids, so the PC party has a better chance to win if three of them just run away ...
There are three possible conclusions to be drawn from this. (1) The CR system as a whole is flawed. (2) The CR's for animals are too high. (3) Druids are unbalanced compared to the other PC classes-they need to have their animal companion ability removed or toned down to bring them in check.
If you've played much 3rd Edition D&D, I'm sure you'll agree that (3) is false. (Actually, it may be true for 1st level druids, as I mentioned above. If a wolf, on its own, is a credible threat to a whole 1st level party, then a party member with a wolf companion, even with poor armor and weapon selection and limited spell capacity, is probably a bit overpowered.) (1) and (2) are both true to an extent. I really don't see a typical 4th level party being significantly challenged by a brown bear. Smart tactics, especially smart use of missile weapons and the speed of the mounts they certainly ought to have at that level, should bring that bear low fairly quickly. (Of course, standing toe-to-toe in melee with it is probably fatal to the party just as quickly, but if they've survived to 4th level they should have a good idea of when not to do that.) CR3 might be more appropriate ... Anyway, it's still a useful object lesson in not being too slavish in following the published CR's. At minimum, a DM needs to pay attention to the guidelines on page 167 under 'Modifying Encounter Levels'. This will solve 90% of the problems with CR's, if used appropriately.