Does fly have two meanings?

Yes, fly has two main meanings, but actually many more than two, so while it is often said fly has two meanings as verb and noun, it has dozens of dictionary definitions. The two most common meanings are as verb meaning to move through air with wings or in aircraft, as in birds fly, planes fly, and as noun meaning small flying insect with two wings, as in housefly. These are two primary meanings that cause pun like time flies like an arrow, fruit flies like a banana. However, fly has many other meanings beyond these two, including as noun meaning zipper flap on pants, artificial fishing lure, fly ball in baseball, and as verb meaning to flee quickly, to display flag, to operate aircraft, and as adjective in slang meaning stylish, cool, attractive, and as noun in theater meaning space above stage. So fly does have two main meanings, verb to move through air and noun insect, but it has many more meanings depending on context, part of speech, and slang, making it highly polysemous word with over 20 definitions in some dictionaries, so yes it has two meanings but actually many more.