The Gnostics taught that matter was evil and that only spirit was good. Because of this teaching many were led to "deny" the flesh entirely. They promoted abstinence from marriage and prolonged fasting. Some of these groups, on the extreme edges, practiced "self mortification" a practice that involved whipping oneself to deny any stronghold to the flesh. Paul's sensible response (v 4) "for everything created by God is good and nothing is to be rejected, provided it is received with thanksgiving" reminds us, once again, everything in creation has a use and a purpose when utilized appropriately, in moderation and in the right context.
The rest of the chapter is a series of words of encouragement for his young disciple.
1. Keep your wits about you and don't go chasing after "profane myths and old wives tales" (6) -- I was once told by a friend of mine to "never wrestle with a pig -- the pig will enjoy it and you'll just get dirty."
2. To train in godliness -- spiritual disciplined living is the mark of a leader and a disciple of Jesus (7/8)
3. Don't let people despise you because you are young -- apparently Timothy is a much younger man -- he is told to set an example. A word to the wise for all of us but especially to younger Christians who may feel slighted or overlooked by their elders -- keep at it, keep fighting, use your gifts, do the work.
4. Do the work of ministry -- read the Scriptures publicly; exhort, teach -- use the spiritual gift that God has given you -- good advise for any and all Christ followers.