How would I add a hotkey to this fly script?

Since Mouse.KeyDown is deprecated, you must use UserInputService. Also, I remade your code to look nicer and more readable.

local UserInputService = game:GetService("UserInputService")

local Player = game.Players.LocalPlayer
local Character = Player.Character or Player.CharacterAdded:Wait()
local HumanoidRootPart = Character:WaitForChild("HumanoidRootPart")

local e1
local e2
local Fly = false
local Speed = 0
local keys = {a = false,d=false,w=false,s=false}

local function start()
	if not Fly then
		Fly = true
	else
		Fly = false
	end
	
	local pos = Instance.new("BodyPosition")
	local gyro = Instance.new("BodyGyro")
	
	pos.Name = "EPIXPOS"
	pos.maxForce = Vector3.new(math.huge, math.huge, math.huge)
	pos.position = HumanoidRootPart.Position
	gyro.maxTorque = Vector3.new(9e9, 9e9, 9e9)
	gyro.cframe = HumanoidRootPart.CFrame
	
	pos.Parent = HumanoidRootPart
	gyro.Parent = HumanoidRootPart
	repeat
		wait()
		Character.Humanoid.PlatformStand = true
		local new = gyro.cframe - gyro.cframe.p + pos.position
	if not keys.w and not keys.s and not keys.a and not keys.d then
		Speed = 1
	end
	
	if keys.w then
		new = new + workspace.CurrentCamera.CoordinateFrame.lookVector * Speed
		Speed=Speed+0.01
	end
	
	if keys.s then
		new = new - workspace.CurrentCamera.CoordinateFrame.lookVector * Speed
		Speed = Speed+0.01
	end
	
	if keys.d then
		new = new * CFrame.new(Speed,0,0)
		Speed=Speed+0.01
	end
	
	if keys.a then
		new = new * CFrame.new(-Speed,0,0)
		Speed = Speed+0.01
	end
	
	if Speed > 5 then
		Speed = 5
	end
	
	pos.position=new.p
	
	if keys.w then
		gyro.cframe = workspace.CurrentCamera.CoordinateFrame*CFrame.Angles(-math.rad(Speed*15),0,0)
	elseif keys.s then
		gyro.cframe = workspace.CurrentCamera.CoordinateFrame*CFrame.Angles(math.rad(Speed*15),0,0)
	else
		gyro.cframe = workspace.CurrentCamera.CoordinateFrame
	end
	
	until not Fly
	
	if gyro then gyro:Destroy() end
	if pos then pos:Destroy() end
	flying = false
	Character.Humanoid.PlatformStand=false
	Speed = 0
end

UserInputService.InputBegan:Connect(function(Input, GameProcess)
	if GameProcess then return end
	if not HumanoidRootPart or not HumanoidRootPart.Parent then flying = false e1:disconnect() e2:disconnect() return end
	if Input.KeyCode == Enum.KeyCode.W then
		keys.w = true
	elseif Input.KeyCode == Enum.KeyCode.S then
		keys.s = true
	elseif Input.KeyCode == Enum.KeyCode.A then
		keys.a = true
	elseif Input.KeyCode == Enum.KeyCode.D then
		keys.d = true
	end
end)

UserInputService.InputEnded:Connect(function(Input, GameProcess)
	if GameProcess then return end
	if not HumanoidRootPart or not HumanoidRootPart.Parent then flying = false e1:disconnect() e2:disconnect() return end
	if Input.KeyCode == Enum.KeyCode.W then
		keys.w = false
	elseif Input.KeyCode == Enum.KeyCode.S then
		keys.s = false
	elseif Input.KeyCode == Enum.KeyCode.A then
		keys.a = false
	elseif Input.KeyCode == Enum.KeyCode.D then
		keys.d = false
	end
end)

UserInputService.InputBegan:Connect(function(Input, GameProcess)
	if GameProcess then return end
	if Input.KeyCode == Enum.KeyCode.F then -- Change "F" to the letter for activating the fly
		start()
	end
end)

If it helped, accept the answer! :D