While you won't find a wide variety of churches in Athens, you will find many Greek Orthodox churches. In fact there are several squares with multiple churches all around them. Feel free to wander in, but be respectful of the dress codes, and of those worshiping. While there are many churches, there are two churches worth noting.
The first is Metropolitan Cathedral of Athens; this church is the main Greek Orthodox Church in Athens, however it is not in use. During the powerful earthquake 1999 this church suffered huge damages, and has since been filled with extra supports and scaffolding. There has been a great deal of effort to try and figure out how to fix the church, but at this point no one is really sure how to go about it. You can walk into the front of the church and check out some of the items that remain, as well as see how this church is being held up.
The other church worth visiting is St George on Lykavitos Hill. This church truly has the best view of Athens since it is perched on top of the tallest point in the whole city. The church itself is fairly small but still very pretty. The bell tower is also very simple, but a great place to get a photograph with the city bellow. If you are able, I recommend walking up, however there is a road and a cable car that will take you most of the way up.
The churches in Athens are very different than those found on the islands, but still well worth investigating.