I found a good explanation here:
To summarize it:
In case of 1 layer design (RootCA issues endpoint certificates) - it´s not recommended due to obvious reasons.
In case of large and expensive 3-layer design, you get great scalability, you can enforce different CA policies on each of the off-line Intermediate CA, you can revoke part of your PKI "tree" and still work fine with the rest.
It is used by worldwide known CA brands, like GoDaddy, Symantec, Thawte, ...
In case of 2 levels, it is a compromise between both. Usually it is used for internal company needs, for company PKI. RootCa is preinstalled only on company PCs. It is relatively cheap, well managable by 2-3 persons and still scalable. You can have IntermediateCA level of online CAs, which you use for issuing internal domain certificates, VPN certificates, 3-party access certificates, ... - each CA with different policy.