I did the trek from Salkantay to Machu Picchu back in 2004 when it was legal to hike independently. It’s the main alternative to the Inca Trail.
Later the incredibly incompetent and corrupt Peruvian government opted for a clumsy cash grab. They pocket whatever money they can extort in a “trekking fee”, and put very little back into protecting the trails. On some trails, including this one, they demand you sign on with a trekking company — quality varying from excellent to absurd.
Many hikers want to trek independently. And a few prefer to avoid the small fee.
From SkateVert:
My wife and I recently hiked the Salkantay Trail to Machu Picchu without a guide. The Peruvian government has now made it a requirement to pay an entrance fee to hike the Salkantay trail. We managed to avoid the fee. Here are some tips …
read the entire trip report on TravelBlog.
Many, many trekkers do this route alone. It’s not difficult. Avoiding altitude sickness is a much bigger concern.
details on our Salkantay to Machu Picchu information page
besthike.com 
This really is my dream destination. Would you say the Salkantay or Inca Trail is better?
By far the best way to get to the ruins is via Choquequirao.
Next time I go, it will be by this route:
http://www.besthike.com/southamerica/peru/choquequirao.html