Yes, but a Bitcoin transaction is secured by the miners whereas an LN transaction is not. Miners serve a purpose, and not only in relation to the security of an individual transaction.
It is said that Bitcoin is deliberately hard to change (as we are finding out).
If in the future the majority of transactions are LN transactions then we are all primarily LN users, not Bitcoin users, and we are at the whim of the LN developers who have complete control to change the protocol that everyone is using to suit themselves.
What's more, as explained here:
http://news.8btc.com/be-firmly-and-openly-against-segewit-and-lightning there is a possibility that LN protocol may also work with other blockchains. At this point LN is not a second layer on top of Bitcoin, LN is the primary protocol and Bitcoin is one of a number of possible second layers on top of LN; This destroys scarcity, since any number of blockchains and coins can be used within the primary network that people are using, and therefore also destroys Bitcoin as a store of value.
