A comparison probably can be made between Ethereum and Hyperledger Fabric (one amongst the many Hyper ledger project).
The most fundamental difference between Ethereum and Hyperledger is the way they are designed and their target audience. Ethereum with it's EVM, smart contract and public block chain is mostly targeted towards applications that are distributed in nature and are for mass consumption. A look at ethereum dapps (distributed applications) seem to hint the same: https://dapps.ethercasts.com/.
On the other hand, Fabric has a very modular architecture and provides a lot of flexibility in terms of what you want to use and what you don't. It's pretty much ala carte and is targeted at businesses wanting to streamline their process by leveraging blockchain technology.
For example, it is not possible in ethereum to have a transaction visible to someone, but not visible to others (a requirement that is very common in business). Fabric allows this and much more.
Another major difference is the consensus algortihm used in Ethereum v/s Fabric. Ethereum uses PoW (Proof of work), whereas Fabric allows one to choose between No-op (no consensus needed) and PBFT (Practical Byzantine Fault Tolerance). PoW is known to be energy sucker and could really impact the practicality of using Ethereum in the long run. However, one must mention that Ethereum too is trying to move towards proof of stake in it's next release Casper.
Ethereum has a built in cryptocurrency (eth) and thus can be a very good match for applications that need this inbuilt. However, this could also be a disadvantage as there are several use cases where the cryptocurrency is not really needed.
This is not to say that Ethereum can not be deployed as a private block chain for a business. The fact that it has a really matured ecosystem and makes the development of smart contract and business logic really simple is a huge plus. Also, at the moment it is easier to find ethereum dapps developer than fabric developer. Fabric on the other hand is pretty new on the block and just warming up.
To conclude, we feel that in future most enterprise apps would get tilted towards Fabric, whereas Ethereum would continue to be a hotbed for dapps that are more B2C.