Why isn't the surface flat?

There is force of adhesion between the molecules of glass and water. Water is made up of polar molecules, which have positively and negatively charged ends. Since opposites attract, the positive sides attract the negative sides, and all of the molecules stick to one another. Glass molecules also happen to be polar. Again, since polar molecules like to stick together, the water in a glass tube will actually tend to stick to the sides of the tube!

Since the meniscus is concave, we can conclude the bonding force (adhesion) between the glass and water is stronger than the surface tension (attraction of the liquid molecules to each other or cohesion) of the water. If the meniscus were convex, the answer would be the 2nd one (surface tension of the liquid would be greater than the adhesive force between the glass and the liquid).

Well, talking about the chemistry, it is not a bonding that happens between water and glass. Adhesion is the word that should have been used. Adhesion forces between water and glass are greater than the cohesion amongst the water molecules which causes the surface to be concave.

"Some containers may attract water molecules much less. Many kinds of plastics, called "hydrophobic", (e.g. teflon) have very small adhesive forces with water , and if you make a container out of these you will get a convex meniscus with water, too." {Quoted from the website.}

Because of difference between convex and concave that can both happen, we realize that difference of atmospheric effects is not the answer.