Mining Bitcoins with anything other than a purpose-designed ASIC is inefficient with the current hash rate, and is unprofitable in terms of power expended and daily profit. But mining coins using the Scrypt algorithm with graphics cards is profitable in a small or large operation.
Why is Scrypt Mining Profitable?
To simply put it, Scrypt requires more memory than SHA hashing and memory is expensive. GPU mining is popular and profitable, because it has large banks of memory standard and cheaply ($300-$400 a card). SHA hashing is easy to do with an ASIC chip because it can be done with very low memory and very inexpensively in terms of resources. So, building an ASIC to do the job of Scrypt mining is a lot more complex and expensive – keep in mind the designing a Bitcoin ASIC was a multi-million dollar process. Having large banks of memory on your ASIC chip introduces a lot more design issues. ASICs for Scrypt is very doable, but a lot less doable than Bitcoin ASICs. We probably will see the rise of Scrypt ASICs within 5 years or less.
What is Scrypt?
It is the hashing algorithm a majority of the cryptocurrencies use. Litecoin, Dogecoin, etc are all Scrypt-based coins. People use Scrypt for good reason, it makes ASIC mining tough, and that's about it. Bitcoin using SHA-256 is not bad in any way, but it's a lot more sensible to use Scrypt with any new altcoin to avoid getting ravaged by extreme hash rates ASICs can impose. And Bitcoin cannot simply change over from SHA-256 to Scrypt either.
When is ASIC Mining Profitable?
Don't get fooled into thinking Bitcoin mining is not profitable, the profit comes with large operations. Say you could get your hands on a few racks of ASICs mining Bitcoin, you'd have reasonable returns. You also have to move fast with Bitcoin, certain ASICs obsolete fast. You start turning a profit with ASICs when you've spent tens of thousands dollars. The BFL units that cost around $250 became inefficient within a few months of release, and you could find units going for thousands of dollars because those were one of the first few shipped early. See http://motherboard.vice.com/blog/a-guide-to-bitcoin-mining-why-someone-bought-a-1500-bitcoin-miner-on-ebay-for-20600