Currently, fruit is the best food source by far. It is the only one that can handle 2 houses worth of population, and can do so with relatively few production slots. You can survive one house with a vegetable/fruit mixture, but not a mix of all three. (Built too many houses before I could test meat enough)

The two options I see for this are to nerf fruit or give health/happiness bonuses for food variety.

Food consumption is calculated as follows:
baseConsumption = Total population / 10000

desiredVegetables = baseConsumption * 0.5
desiredFruit = baseConsumption * 0.3
desiredMeat = baseConsumption * 0.5

First it checks for fruit, if the amount of fruit available is enough to cover desiredFruit then all is well.
If there's not enough fruit, the desiredFruit value gets offloaded onto desiredMeat.

So, if there's no fruit, desiredMeat is now baseConsumption * 0.8.

It does the same thing for meat next: If there's enough to cover desiredMeat, all is well!
If there's not enough it adds desiredMeat to desiredVegetables.

So if there's no meat, desiredVegetables is now baseConsumption * 1.0

This also means if there's no fruit, desiredVegetables = 1.3.

And finally, if there are not enough vegetables to cover desiredVegetables (Which can now hold the values of fruit and meat as well!), people enter starvation and being dying off.

Having enough of each type of food means each source is consumed the least. Missing a food source, means other sources are over-consumed to make up for it.