I only read the first Dune novel, when I was in college, several years before I got interested in Islam. It was my first exposure to the Arabic language, and gave me a head start when I first began to learn Arabic. Then I went back to Dune and figured out Herbert’s little linguistic games with Arabic. These are just the ones I remember off the top of my head without looking them up:
Muad’Dib—the Mouse in the Moon?
Huh?
I never did get what that had to do with anything. But mu’addib (the correct spelling) is a real Arabic word, and it means ‘one who inculcates good manners and cultural refinement (adab)’. Which sort of describes Paul’s role.
La, la, la—No, no, no! I had studied a little Hebrew before reading Dune and could instantly see the relation of Hebrew to Arabic. Lo I knew was Hebrew for ‘no’. Shalom/salâm: so Hebrew o corresponds to Arabic â.
Lisan al-ghayb—literally ‘tongue of the Unseen’; Herbert was accurate in glossing this. Actually, Lisân al-ghayb is the epithet for the great Persian poet Hâfiz.
Gom jabbar—The phrase qawm jabbâr (the correct spelling) literally means ‘a powerful, oppressive nation’. It actually occurs as such in the Qur’ân, in verse 5:22, referring to the peoples occupying the Promised Land when Moses brought the Israelites there. Herbert’s translation as ‘high-handed enemy’ is obscure. Applying it to a poisoned needle is even more obscure.
Alia—feminine form of the name ‘Ali meaning ‘high’. A genuine Arabic girl’s name. Also familiar as the name of late pop star Aaliyah, using a different spelling, but the same name.
Feyd Rautha—Arabic for ‘overflowing abundance of horse-poop’. 
Shai Halud—if the second word could be read as hulûd (i.e. khulûd), this might mean ‘Thing of immortality’.
Bene Gesserit—Hebrew for ‘Children of the Bridge’(?). This may not be very exact Hebrew, but gesher means ‘bridge’, related to Arabic jisr.
I certainly didn’t get any negative impressions of Islam from reading Dune. On the contrary, the Fremen are good guys, freedom fighters; it was one of the first positive impressions of Arabs I ever got from literature.