If you take a look at the dimensions of your data you will notice that it is wrapped into an additional layer (which could mean that it is kind of a 3D structure --- list of data):

data = Import["~/Downloads/test.nc",  {"Datasets",  "SST"}]; 
Dimensions[data]

(* ==> {1, 801, 1001} *)

So what you want to do here to plot the data, is getting rid of additional layer, which can be done as easy as:

data = First[data]; 
Dimensions[data]

(* ==> {801, 1001} *)

Now you can plot the data:

ArrayPlot[data]

Or you could plot it as it is:

ArrayPlot /@ data

All the rest, in the example from the documentation I refereed to, is matter of preference. For example here is how it looks when you reverse your data:

ArrayPlot[Reverse[data]]

Or, here is how the ColorFunction actually influences your plot:

ArrayPlot[Reverse[data],  ColorFunction -> "BlueGreenYellow"]

And so on, so force.

p.s. Please consider removing External Programs and Systems from your question's keywords, since it is not related to your question.

Alike example can be found in the documentation:

data = Import["ExampleData/precipitation.nc", {"Datasets", "ANOMALY"}];
ArrayPlot[Reverse@data, PlotRange -> {-2, 2.5}, ColorFunction -> "ThermometerColors", ImageSize -> Medium]

This is taken from NetCDF, which I strongly recommend you going through.