Some .meta files contain important information.
For example, this is part of a .meta file for a .png file in our project:
fileFormatVersion: 2
guid: a652b1795b650454a8270045af8e2a71
timeCreated: 1459880238
licenseType: Pro
TextureImporter:
fileIDToRecycleName: {}
serializedVersion: 2
mipmaps:
mipMapMode: 0
enableMipMap: 0
linearTexture: 0
correctGamma: 0
fadeOut: 0
borderMipMap: 0
mipMapFadeDistanceStart: 1
mipMapFadeDistanceEnd: 3
bumpmap:
convertToNormalMap: 0
externalNormalMap: 0
heightScale: 0.25
normalMapFilter: 0
You can see there are a lot of settings that tell Unity how to use the associated .png
file.
If you delete this .meta file, it will regenerate it, but you'll lose any import settings you had set. It can cause other issues, but just this example should be enough to convince you to leave them alone. :)