I've setup a couple of ecommerce sites myself in this country and I can attest to the problems.
1. The payment processors are unhelpful sharks - to actually get a merchant account to take online payments is a bureaucratic nightmare and if you don't get a merchant account you have to work through a third party like setcom/paypal/etc which is a joke as they either demand a huge percentage of your sales or hassle you about releasing the money and happily reverse any and every transaction a customer queries, no questions asked. Most of the online payment gateways are also very technically unflexible - i.e. Setcom will only let you add one item at a time to the shopping basket - you either have to bounce your customer to their site with every "click to add to cart", or you have to combine everything into one item at the end of the process.
2. Fraud - one ecommerce site I was involved with at one point had a ratio of 5 fraudulent attempted credit card transactions for every valid one. The result is that the shopowners were terrified to despatch anything (high value electronics) because of the danger that the transaction could turn out to be with a stolen card or could be disputed and reversed in 2 months time.
3. Bandwidth - apart from the fact that bandwidth is already way overpriced, unless you have the expertise to co-locate your own server at somewhere like hetzner where you'll pay a good rate for fast bandwidth, you will probably end up being raped for hosting by anyone of the many unscrupulous providers out there.
4. Shipping - just costing this and pricing it into the sales order is a nightmare. Forget about international shipping! Expect endless meetings with local courier companies and still end up scratching your head about how to do this and be competitive. Unlike overseas where you can simply plug your ecommerce application into a web service run by your favorite courier company to get realtime pricing, etc for the item, almost all the local couriers have no clue what you're on about. Then work out how you can sell a R50 item online when the shipping will cost you R56. Since shipping is by generally weight forget sending anything like a computer box or large crt monitor.
5. Bureaucratic legal mumbo jumbo and regulations - thanks to the ECT act etc, if you want to cover your backside properly, you have to hire a lawyer to draft the right privacy policy, disclaimers and paia documents for your website as well as ensure that you have the right policies regarding cooling off periods and allowing customers to refund goods, otherwise you could potentially end up in hot water with the law. There is no real distinction whether you're a hobbyist selling a few things not for profit or a large corporate entity. Just out of interest - according to a new international tax treaty, if you sell to the EU you now have to charge the right VAT depending on which country in the EU the customer is and it's your responsiblity that the customer is where they say they are.
I'd say that the majority of eager online entrepreneurs drop out of the process when they start to find out about all of these things. Others (depending on the product) take it all offshore to server in Panama where they don't have to give a damn about regulations, taxes and bureaucracy and you can become a Panama citizen overnight simply by sending a cheque.