Have you seen how much opening a lightning channel cost? And opening a second channel, if you cannot find a route to your merchant? How about refilling your channel? Or how to close it, if a malicious node wants to steal your funds?
That's right, it will all cost the same as a Bitcoin transaction.
And how about receiving a lightning payment? Well... The merchant need to have a balance so he can accept your payment(!) Yes, that's another Bitcoin transaction right there. Or if you're lucky you can find someone who'll give you liquidity (for a fee of course).
It's debatable if micropayments will ever take off, but lightning never will.