As far as I have understood your query, it seems that you are not providing the GTA services directly. Rather you are arranging transport facility for your client and are charging some amount of commission on the transporters bill. Hence you are actually an agent to your customers, or say the person liable to pay freight is paying freight through you. If we go through the relevant rules i.e., Rule 2 (1) (d) of Service Tax Rules, 1994:” "Person liable for paying service tax" means,-
(v) In relation to taxable service provided by a goods transport agency, where the consignor or consignee of goods is,-
(a) any factory registered under or governed by the Factories Act, 1948 (63 of 1948)
(b) any company formed or registered under the Companies Act, 1956 (1 of 1956)
(c) any corporation established by or under any law
(d) any society registered under the Societies Registration Act, 1860 (21 of 1860) or under any law corresponding to that Act in force in any part of India
(e) any co-operative society established by or under any law
(f) any dealer of excisable goods, who is registered under the Central Excise Act, 1944 (1 of 1944) or the rules made thereunder or
(g) any body corporate established, or a partnership firm registered, by or under any law,
any person who pays or is liable to pay freight either himself or through his agent for the transportation of such goods by road in a goods carriage;”
I may be wrong in my opinion but you as an agent are not liable to pay service tax on GTA. I think you are niether consignor nor consignee as per transporter's invoice.You should pass on the liability to your customer. Service Tax on commission is a different issue here. Moreover, even if my opinion happens to be wrong and you are not covered by the category defined above, the liability of service tax will be on GTA and not on you.
Hope this is helpful. Other members are requested to correct my opinion if I am wrong.