They are heritable just like heritability of, say, home or fortune. Home the children live in is not influenced by genes, but is still heritable.
That explanation fails as a home is only passed on to one child, if at all. The microbes are passed on to all offspring. I do not doubt that the microbes are passed on, just that they are considered heritable. On the other hand, if there is a condition or environment in the gut of the offspring that allows some microbes to flourish over other microbes, then that would be heritable. But, the microbes, themselves are not heritable.
They are transferable, but not heritable. For instance, if in vitro fertilization is used and the embryo implanted in a surrogate mother, the microbes that are transferred are from the surrogate, not the biological mother. The offspring inherits the gut environment that might allow one type of microbe to flourish over another, but not the microbes themselves.
This is further evidenced by the fact that identical twins end up with the same microbes, but fraternal twins do not. The mother, as do we all, have most of the microbes in question. It is a matter of which ones can thrive. Identical twins end up with identical guts, fraternal twins do not. As such, identical twins end up with the same flora, but not necessarily for fraternal twins (they may end up with similar gut environments).
In short, it is the gut environment that allows for certain microbes to flourish over others that is heritable, not the microbes themselves.