As a supplement to Frank Luke's answer, I add another way of thinking about it.
The construction in English is very similar to the Greek: not X, but [instead] Y. (Wallace calls ἀλλὰ here a contrastive conjunction.1)
For example, if I say
"Put not your hand into boiling water, but use a spoon."
The contrast is between:
X= put your hand into boiling water
Y= use a spoon
Notice that X does not contain the negation.
In Matthew the contrast is between:
X= lead us into temptation
Y= deliver us from evil
Again, the particle of negation is not part of X.
For another example of a similar construction in Matthew, see Matt 5:17b (ESV)
I have not come to abolish [the law or the prophets] but to fulfill them.
X= to abolish
Y= to fulfill
1. Daniel B. Wallace, Greek Grammar Beyond the Basics: An Exegetical Syntax of the New Testament (Grand Rapids, MI: Zondervan, 1996), 671.