Why is my keydown function working when the tool is unequipped?

You need to actually make sure the tool is equipped before you process the user input. Added lines 8, 10, 16, and 27 - 32.

repeat wait() until game.Players.LocalPlayer.Character
local Player = game.Players.LocalPlayer
local Body = Player.Character
local Mouse = Player:GetMouse()
local Level = script.Parent.Level.Value
local Cash = Player.leaderstats.Cash
local Tool = script.Parent
local ToolIsEquipped
script.Parent.Activated:connect(function()
    if not ToolIsEquipped then return end
    local Destination = Mouse.Hit
    wait(5 - Level)
    Body:MoveTo(Destination.p)
end)
Mouse.KeyDown:connect(function(k)
    if not ToolIsEquipped then return end
    k = k:lower()
    if k == "r" then
        if Level < 5 then
            if Cash.Value >= (Level * 5) then
                Cash.Value = Cash.Value - (Level * 5)
                Level = Level + 1
            end
        end
    end
end)
Tool.Equipped:Connect(function()
    ToolIsEquipped = true
end)
Tool.Unequipped:Connect(function()
    ToolIsEquipped = false
end)