Most examples of neural networks for classification tasks I've seen use the a softmax layer as output activation function. Normally, the other hidden units use a sigmoid, tanh, or ReLu function as activation function. Using the softmax function here would - as far as I know - work out mathematically too.
I haven't found any publications about why using softmax as an activation in a hidden layer is not the best idea (except Quora question which you probably have already read) but I will try to explain why it is not the best idea to use it in this case :
1. Variables independence : a lot of regularization and effort is put to keep your variables independent, uncorrelated and quite sparse. If you use softmax layer as a hidden layer - then you will keep all your nodes (hidden variables) linearly dependent which may result in many problems and poor generalization.
2. Training issues : try to imagine that to make your network working better you have to make a part of activations from your hidden layer a little bit lower. Then - automaticaly you are making rest of them to have mean activation on a higher level which might in fact increase the error and harm your training phase.
3. Mathematical issues : by creating constrains on activations of your model you decrease the expressive power of your model without any logical explaination. The strive for having all activations the same is not worth it in my opinion.
4. Batch normalization does it better : one may consider the fact that constant mean output from a network may be useful for training. But on the other hand a technique called Batch Normalization has been already proven to work better, whereas it was reported that setting softmax as activation function in hidden layer may decrease the accuracy and the speed of learning.
Softmax layers can be used within neural networks such as in Neural Turing Machines (NTM) and an improvement of those which are Differentiable Neural Computer (DNC).
To summarize, those architectures are RNNs/LSTMs which have been modified to contain a differentiable (neural) memory matrix which is possible to write and access through time steps.
Quickly explained, the softmax function here enables a normalization of a fetch of the memory and other similar quirks for content-based addressing of the memory. About that, I really liked this article which illustrates the operations in an NTM and other recent RNN architectures with interactive figures.
Moreover, Softmax is used in attention mechanisms for, say, machine translation, such as in this paper. There, the Softmax enables a normalization of the places to where attention is distributed in order to "softly" retain the maximal place to pay attention to: that is, to also pay a little bit of attention to elsewhere in a soft manner. However, this could be considered like to be a mini-neural network that deals with attention, within the big one, as explained in the paper. Therefore, it could be debated whether or not Softmax is used only at the end of neural networks.
Hope it helps!
Edit - More recently, it's even possible to see Neural Machine Translation (NMT) models where only attention (with softmax) is used, without any RNN nor CNN: http://nlp.seas.harvard.edu/2018/04/03/attention.html
Use a softmax activation wherever you want to model a multinomial distribution. This may be (usually) an output layer y, but can also be an intermediate layer, say a multinomial latent variable z. As mentioned in this thread for outputs {o_i}, sum({o_i}) = 1 is a linear dependency, which is intentional at this layer. Additional layers may provide desired sparsity and/or feature independence downstream.
Page 198 of Deep Learning (Goodfellow, Bengio, Courville)
Any time we wish to represent a probability distribution over a discrete variable with n possible values, we may use the softmax function. This can be seen as a generalization of the sigmoid function which was used to represent a probability distribution over a binary variable. Softmax functions are most often used as the output of a classifier, to represent the probability distribution over n different classes. More rarely, softmax functions can be used inside the model itself, if we wish the model to choose between one of n different options for some internal variable.
Softmax function is used for the output layer only (at least in most cases) to ensure that the sum of the components of output vector is equal to 1 (for clarity see the formula of softmax cost function). This also implies what is the probability of occurrence of each component (class) of the output and hence sum of the probabilities(or output components) is equal to 1.
