IBS
 "for bodily exercise profiteth little: but godliness is profitable unto all things, having promise of the life that now is, and of that which is to come."

So one day our bodies are going to be decomposing in the ground so all the effort we put into building up our bodies is not going to last, but our Spirit will live for ever so we ought to build that up instead. Not that we shouldn't exercise our bodies, but it only profits a little. Actually Now that I'm thinking about it and am looking at the context I don't think Paul is writing about working out, and that that assumption might just be me presupposing my own experiences and culture into the text, but I think he's talking about outward actions in general, particularly ones having to do with spiritual progress. In verse 3 he writes about those that will depart from the faith in the future, who will tell others not to marry and to obstain from certain foods, which are outward practices, bodily exercises that profit only a little

I think it was Augustine who once said  "what good is it to abstain from wine when one is intoxicated with anger" abstaining from wine is a bodily exercise and is profitable for sure, but anger has to do with the inner man, with our Spirit, it is much more profitable to abstain from anger than from wine. Drinking wine becomes unprofitable when it affects our inner man, when it causes us to lust or be angry. So sure abstain from wine or relationships or foods or whatever, it will help some, but most importantly exercise yourself to be godly, which consists at first in the invisible world of thoughts and feelings. The Pharisees were all bodily exercise and no godliness. Jesus said not only to not commit adultery physically but equally as important to not commit adultery in your heart. Godliness has to do I think  with character. So yeah I think he's just tryna say we ought to "look not at the things that are seen but at the things that are not seen, for the things that are seen are temporary but the things that are not seen are eternal"

Application
I'm not going to look at outward obedience or bodily exercise as success, simply not acting on my wrong desires, but I will seek godliness by having the correct heart, by not giving in to wrong things in my heart, I will do this by prayer and depending on God, coming to Him empty handed and unable